Smite is aimed at the bag of holding. Not at the boss itself.
Going by the rules. When a bag of holding is destroyed. The contents contained within are scattered to the Astral Plane.
Boss isn’t fully inside the bag and so isn’t its contents.
Now… if this was the disembodied head of Nixon in a jar that’d be another matter.
Aroooooo!
Yeah. This was quite amusing on Dungeons & Daddies but I wouldn’t allow it either. Essentially 1 Sleight of Hand or Athletics roll plus an attack roll with advantage (blind) shouldn’t equal an instant kill even if it destroys a magic item.
I would argue that the contents get drawn in, but since he is not even half in there he would just take a lot of force damage and the bag gets destroyed. (and maybe the boss is bald afterwards and lost their hat)
Would closing a gate and thereby bisecting a being also bisect their soul?