There is a general bug where items higher on a wall are only lootable on the next floor up. The burning inn has quite a few of those. In no particular order: 2 paintings (paintings are lootable and worth a decent amount); all of the drinks on the shelves/walls in the alcove to the left of the bar (looking from the entrance); all of the drinks on the shelves/walls in the alcove furthest to the left/front of the inn (first floor); and the book, wine bottle, and row of books at the top of the stairs. There are others but I can't remember them off the top of my head.
Yes, I loot Waukeen's Rest for all it will give, which is a huge amount of drinks, a decent amount of food, and a few sellables/collectibles like the paintings. If you are going to do that, I suggest collecting water barrels and bottles up until that scene - you will use a lot of them suppressing fires. And going to turn-based time helps too, but beware the bugs: https://forums.larian.com/ubbthreads.php?ubb=showflat&Number=745482#Post745482