Really? I thought those were terrible. Basically it was impossible using these rules to have a business that was profitable. All the rules did was provide yet another money sink for the pcs and maybe the occasional adventure hook.
I played in a game where my character stumbled into possession of a whore house. It lead to an entertaining subplot about competition with a rival whore house. Soon after, the campaign collapsed into farce.
I'm of the opinion that, if your players establish a business, the GM is probably being too soft on them. He's giving out too much loot, and allowing them to become too comfortable. (How did they get all that loot in the first place? If they found "the mother load" in some dungeon, how did they carry it all out?). I think the GM is setting a precident which will eventually kill the campaign. Unless the business venture is short lived.
If a PC or PCs are intent on starting a business, the business should be HARD and require a lot of effort. If it's an individual PC, his job should routinely prevent him from traveling with the adventuring party. If the whole group is involved, they should have constant challenges related to the business.
I would stress the mundane aspects of business operation. Again, where do they keep their money? How does a group with 20,000gp in assets effect the local economy: i.e. inflation! Adventurers should not make good businessmen. Let them try to sort out management issues, like dealing with interpersonal conflict between workers, labour strikes, supply shortages, zoning violations, etc. Eventually, their volatile tendencies will get them into trouble and make their business unpopular and unsuccessful. The adventurers will cut their losses, burn the place down, and return to the life less ordinary.
As for owning a theive's guild, that's slightly different from owning a business. It's actually a very good way to introduce adventure hooks. But, like a business, it shouldn't be easy to run a theive's guild. It would probably be the hardest job imaginable, because you can't trust anybody. The leader of the theive's guild probably wouldn't be able to sleep at night for fear of a knife to his throat. And, ah, he will probably get it in the end.
Personally, I have a preference for desperate, low-magic, low-wealth, Dark Ages-style campaign settings where things like this could never happen. I don't like big glistening fantasy cities with law and order and all that. I think finding food should be a struggle.