Actually, even "wealthy" people in Medieval life rarely had money on-hand. At least, cash-money - they usually had some pawnable silverware or something. Even large money transfers were done by accountants at the local monastery purely on paper.
In fact, part of why Europe's counties are such a mess is that, when gambling, nobles would often gamble their land, which could actually be fairly assessed, rather than money. This resulted in peasants frequently not knowing who was actually their lord that week, since they could have been lost to another neighboring lord over a hand of cards last weekend. For that matter, they frequently didn't particularly care, since the lord mostly only mattered when they collected taxes, and taxation was usually fixed.
It wouldn't be historically inaccurate for someone to come in with nothing but trader credits for use on the next dwarven caravan as payment.
so... Guilds will be fortress run and not independent organizations?
An "academy" might be fortress-run or guild-run. (And if we're going by the model of tutoring or apprenticeship without a formal declaration of academies, there might not even be an academy, just some guy that buys training like a traveler might buy a *dwarven syrup roast [10]* for the road.)
Doing things that rake in money for the fortress as a whole and raise its stature may not result in direct remuneration in a fortress, but may carry with it a ton of fame and respect, which, depending on culture, may be worth more, anyway.
One of the other things covered in
Debt: The First 5000 Years was that civilizations that elect leaders by popular consent (I.E. the mayor) tended to be led by the most materially poor citizens, as they tended to be constantly doing favors and lending things out to maintain their popularity, whereas power through inheritance naturally led to the hoarding of wealth.
Hence, a skilled dwarf might teach and spread word of their works and teaching skill for the social ramifications rather than the wealth. DF is also a world where the afterlife comes to you, in the form of ghosts and Toady has said that afterlives should be visitable, so it's entirely possible for a dwarf to be motivated by their ethics of creating great works of craftsdwarfship over monetary rewards. (And historically, most Medieval artists were driven by religious faith and almost expressly created art devoted to religious themes.) Such workers wouldn't pay much mind to the fortress as a whole taking up their profits.
If the guild is operating as an independent entity, it opens up a different can of worms in that you might be a step removed in its operation. They're simply renting space from you, and you might not control their employees, since you'd be damaging their business if you took back space or resources from them. This can have serious ramifications for the running of your fortress if your fortress has to feed some guild resources, but have only indirect control over what products are spit back out in return. (You really need a half-dozen magma-proof enormous corkscrews NOW, but today, the guild feels like using your steel to make goblets, instead!)
Also,
Would you even consider changing the relationship that the player has with the dwarves right now (as unquestioned overlord and direct allower and denier of all things dwarves can and cannot do), so that dwarves can become more autonomous and individual, and possibly create a better simulation, while on the other hand, potentially dramatically upping the potential for Fun because dwarves are stupid and very likely to hurt themselves unless continually babysat, or perhaps more importantly, if it meant that the player had less direct control over his fortress, and had to rely more on coaxing the ants in his/her antfarm to do his/her bidding?
Our eventual goal is to have the player's role be the embodiment of positions of power within the fortress, performing actions in their official capacity, to the point that in an ideal world each command you give would be linked to some noble, official or commander. I don't think coaxing is the way I'm thinking of it though, as with a game like Majesty which somebody brought up, because your orders would also carry the weight of being assumed to be for survival for the most part, not as bounties or a similar system. Once your fortress is larger, you might have to work a little harder to keep people around, but your dwarves in the first year would be more like crew taking orders from the captain of a ship out to sea or something, where you'd have difficulty getting them to do what you want only if you've totally flopped and they are ready to defy the expedition leader.
Anyway, a lot of that is stuff I was talking about in Class Warfare... (I really need to go back to that thread soon...)