There are two possible issues here.
1. Monsters always get a to-hit bonus when attacking the player.
If you work through the numbers in the Vade-Mecum's sections on fighting and armor, you'll see that it describes the +4 bonus. See in particular the part about how much AC is needed to block all hits from Hobgoblins. If the mechanics have always been that way, to the point where they're described in the Vade-Mecum, I'm not going to call it a bug.
While the authors may not always have understood why their code did what it did, a 20% increase in monster accuracy has a significant effect, one that they and their lab of playtesters would have noticed. It may have been introduced by accident, but it remained deliberately, and became part of the balance of the game.
I get what you're saying but it should be clear if the original intention was for monsters to get the bonus all the time there wouldn't be any test against ISRUN flag.
Regarding historicity of it, it seems to me you give too much credit to some random people I think we don't know who they actually are, and I don't see a reason why should their version of the game be taken as the reference.
Why not Epyx DOS version be the reference? Even better, Mac or Atari ST versions as they came later and likely were more refined and more bug-fixed, plus they were made by the actual original authors of the game.
2. The player never gets the bonus, even when attacking a sleeping monster.
If this is happening, it is definitely a bug.
It is happening. Simple solution is to move the call to runto() function from the beginning of the fight() function to its end.
This makes it obvious the whole addition of "to-hit bonus" feature in v4 was half-assed. Instead of giving the player slightly better chance of fighting monsters, it made already hard game not just harder but also unfair.
I also think this shows your reasoning regarding historical preservation is flawed. You could just as well say you want to preserve this bug for the same reasons you want to preserve the first bug. The flaw is not in your desire to keep it historically accurate, the problem is in choosing which version to take as a proper historical reference.