I was noticing the same issue with brothels as well - didn't test out the motivation though so that could have been my issue too. For me, only about 4 or 5 of my whores were consistently working even though I had about 10 in the brothel. Will try what you suggested about motivation once per day for a week and see if that solves it.
Also - thank you for rebalancing the legal businesses! I'd tried them in most of my playthroughs but to your point, they always just seemed like a waste of money. I get that the point of the game is to reward the player for being evil, but it's still nice to have options.