Right, the inventory is getting too large. I am overhauling the selling screen in 0.1.15 where it's tile based and with scrolling for the inventory side. Will use a similar look for the inventory itself (in a later patch).
With ground clipping through airship, do you mean terrain on the flight? Or just parts of the tower? In case of terrain, I've never seen that, would need some coordinates and which flight you took.
Shop decorations in the way of entrances: check. This is a remnant of an early prototype of cafes, where entrances weren't a thing yet. Putting it on my list
Tiny houses where you can't access to chest: Seen those, don't have a solution right now. Probably I'll just remove the bed.
As for getting stuck in taverns: haven't really seen that, so I'll need to check. Would be nice if you can drop me the coordinates (seen in the minimap display in the top right).