Hit Points can represent a lot of things

Hit points are often thought of as a sign of how many blows with a weapon will be necessary to take an enemy down. This makes sense when we picture a huge dragon which could be covered with arrow wounds but still a deadly threat: it makes less sense when we are picturing a lone evil wizard or warlord.

But in reality, the mechanics for hit points and damage are not always about how much physical punishment an enemy can take. Hit points are described thusly (PHB, p. 196):

Hit points represent a combination of physical and mental durability, the will to live, and luck.

We are also told that (ibid):

An attack that reduces you to 0 hit points strikes you directly, leaving a bleeding injury or other trauma.

So hit points may do more than represent how much your body can be cut or pierced before it falls: hit points may represent your ability to stop yourself from being "struck directly" at all (until they run out).

If your player attempts to strike the villain "out of combat", (first of all, you should roll initiative), then you could say that the villain digs deep into their "will to live", fights through whatever is "completely restricting" their movement, and twitches at the last second, causing the blade to dig into their collarbone (or even misses them altogether) rather than plunging into their artery. Naturally, such an effort is taxing and can't be done many times (or is just super lucky, and can't be relied on to happen repeatedly): that's why it deducts from their hit points.

Turnabout is fair play

A player may object that such a "twitch" is impossible. Perhaps the villain is under the influence of a Hold Person spell, and the players claim that the villain cannot move at all and must be utterly still. You could make any number of counterarguments to this (e.g. that "paralysis" is relative, since you can apparently still breathe and your heart still beats), but the most powerful one is likely to be that the players wouldn't want this rule to be similarly applied to their characters.

Remind them that next time they are in combat with a bunch of measly goblins, they might have the spell Sleep (which has no saving throw) cast on them. Or they might find themselves attacked at night while most of the party is asleep, and their enemies might cast Silence on the campsite before the first round of combat (which again has no saving throw). And that while one of them is peacefully slumbering on the ground (and is thus unconscious, which has all the in-game disadvantages of being paralyzed), a goblin might use its six second long turn to gingerly and carefully push three inches of the shaft of one of their crude arrows through the player character's eye, and into the brain beyond.

If they don't want that to happen, they'd better agree that the villain can twitch.

If the only reason why the NPC "wouldn't die" is that, mechanically, you can't deal enough damage with a knife to kill him - just ignore the mechanics.

The rules on hit points, damage etc. are meant for combat. If an NPC is entirely helpless, and an (N)PC wants to slit the throat of the NPC, let them.

The rules are just a tool - if, rules-wise, you would have to slit someone's throat 15 times until he dies, then the problem is the rules, not the fact that someone's throat was slit.

Either way, one of the first things the PHB mentions about rolls is that to make a roll, the outcome has to be uncertain in the first place:

In cases where the outcome of an action is uncertain, the Dungeons & Dragons game relies on rolls of a 20-sided die, a d20, to determine success or failure.

_{^{PHB, p. 7, "The d20". Emphasis mine.}}

Do note that, just because you are under the effect of the Restrained condition, trying to slit your throat is not necessarily a guaranteed success. The Restrained condition is very general. It can mean that you've got a tentacle wrapped around you up to your armpits, rendering you immobile and giving you disadvantage on attacks since you're arms are somewhat blocked. Still, you can defend yourself against someone trying to slit your throat.

An example of a situation in which you would be completely defenseless is when you're knocked out cold, or when you're strapped to the kind of operating chair that also restrains your head, found in every second horror or superhero-backstory movie. Be careful with the first example - if you allow auto-kills on unconscious characters (as much sense as it might make), your players will probably start abusing the Sleep spell or similar magic.

Rules are rules

What you're ultimately asking is how to narratively explain game rules. That's a bit tricky at any level and it may be a sign of an immersion problem. Understanding that there are game rules and having to play by them seems to be a bigger table concern. If players are constantly asking "why is this the rule", then they are having trouble immersing themselves into the system with the given constraints (or they want to try and bypass those constraints.)

You shouldn't have to explain why the rules are the rules. You should just be letting folks know there are rules and judging how to apply those rules to any given situation.

The case (or lack thereof) of autohit/autodeath on Paralyzed creatures

In this case, narratively you could just say that the creature was squirming and is still difficult to kill - but not even conditions that should make it extremely easy to one-shot provide that option.

Even a paralyzed creature isn't autokilled or even autohit. Hits are crits within 5', but that isn't an autokill. Even the Rogue Assassin's Assasinate feature doesn't actually assassinate.

Attacking is combat, and combat is generally done within initiative. And it may not be the target that causing the miss...a natural 1 is still always a miss and the attacker could simply have...fumbled.

Based on a comment in PixelMaster's answer, you said:

I also think arguably, for the specific example I provided, an NPC may be allowed ability checks to break free from restraints, putting a time cost on repeated strikes.

This is narrative reason for calling an attack roll in itself. If the NPC is struggling, then hitting the vitals becomes non-trivial. Then, when the PCs are unable to one-shot the enemy, you can say that the player's attacks cut deep, but missed the target's vitals.

Keep the explanation simple and get back to the game.

I occasionally hear, "That would definitely kill someone in real life!" from my players. My standard response is, "In D&D, the laws of nature are different." Just reminding my players that things work differently in D&D than in real life is usually enough to satisfy them. Coming up with a convoluted explanation of how somehow the weapon fails to connect completely takes up time that is better spent continuing the adventure.

If the intended narrative result is that the NPC does in fact die, in contradiction to his hit points and the damage of a knife, then what you're looking for is the coup de grace mechanism. Unfortunately, to the best of my knowledge, there is no such mechanism in 5e.

My response to this, as a GM, is to channel Mr. Bumble:

If the rulebook supposes that, the rulebook is a ass — a idiot. If
that's the eye of the rulebook, the rulebook is a bachelor; and the
worst I wish the rulebook is, that his eye may be opened by experience
— by experience."

The rulebook, however, supports Mr Bumble on page 5 of the DMG:

The rules don't account for every possible situation that might arise during a typical D&D session.

The implication here is that if a coup de grace makes sense, then it makes sense, and you can and should go with it.

If the intended narrative result is to stick to a pure rules-as-written and have the guy survive because there is no coup de grace rule, then you're fairly well stuck. You could, I suppose, rule that the guy broke free just in time and now you're in standard combat rules. This might even be warranted by the NPC's skills. But let's be clear: Just as there is no mechanical coup de grace rule in 5e, there is also no mechanical connection between "Has too many hit points to die from a knife attack," and "Breaks free at the right time," at least not in 5e. (There are some-- much-- more narratively structured games where there might be, but 5e is not one of them.)

The PC could offer a reward for his life. Or you could have the guy rescued. Or the PCs could be distracted at the vital moment by some other can't-ignore happenstance, like orc raiders. Or the PC might have forgotten to sharpen his knife. Or blue bolts from the sky could strike the PC. But these are contrivances, which is why they get more contrived as the examples go on. More importantly, they are also completely mechanically disconnected from the rules for, and idea of, hit points in 5e.

I stress this because I think it is important: There are things you can do, narratively, to get yourself out of this jam. The first three that I gave above are serious or semi-serious. But you should be absolutely clear that this has almost nothing to do with the rules, or the damage roll, or the number of hit points the NPC has, and is more in the vein of a genre convention (a convention of script immunity) that you are enforcing. It is your right and responsibility as a GM to choose and enforce your genre conventions. Just be clear that this is what you're doing, and that you're doing so because of the lack of a special-purpose but common-sense mechanic in the rulebooks.