I actually really dislike the way stealing works in this game. It seems like you can get away with taking anything as long as the owner doesn't have line of sight on you. You can walk into a building, speak with the owner, go around a corner and take everything that isn't nailed down and somehow get away with it. For some reason they can't put together the fact that you were the last person in the room before their pillows were stolen, shields removed from the walls, and collection of potions vanished from the shelves. Your reputation seems go unscathed, and that makes absolutely no sense.
Just out of interest have you played a game where the people put 2 and 2 together and work out that you must have stolen things that they didn't see you stealing? Even in the Elder scrolls games you could steal things right from behind someone if they were facing the other way. That is also possible in rl as well and without some kind of proof how on earth are they going to know that you've stolen their things.
I did always find it weird in Elder Scrolls stealing something from the upstairs in a merchants and then taking it downstairs and selling it back to them. That I think they should be able to pull you up on as they should recognise their own things, but I don't see how they're supposed to know you stolen things they didn't see you take.
Theft in Skyrim was easier to (visually) accept because eventually items that were taken either respawned or were replaced with different items. In Divinity, when you clean out a room it seems to remain that way indefinitely. Tables remain barren, beds are pillowless, etc.
I don't think NPCs should be accusing players of theft when they don't witness it. But I do think reputation scores should suffer and their attitude towards you should lower as more and more items vanish from their homes, especially when the thefts coincide with your visits.
"Whenever Bob pays me a visit, all the paintings on my walls along with my silverware disappears..!" It makes sense that rumors would start to spread.
Anyway, I think a big part of the problems being seen in the original post is the randomness of loot. You can go through several crates and walk out with several hundred gold. Or, you can end up with nothing. That's going to lead to some players struggling to afford gear while others claim to be just fine.
