Going again with the factions request, shop operators
in dungeons probably aren't going to be on too friendly
terms with at least certain monsters - especially those
that aren't intelligent enough to barter with a shop
keeper or those who's goal is to crush all living life
forms. ;-)
Stores should probably be a little better protected,
such as always have strong gates that perhaps
auto-close after a few rounds of time and have a guard
or three that are capable fighters relative to the
dungeon depth.
Dungeon stores should also perhaps be themed, as with
town shops.