I always assumed that, outside the Rep system, the Ultimates would basically have a very tightly regulated command economy, sort of like the economy you'd expect a modern day army to have if its logistics never had to come into contact with the free market. They don't care if they've got fabbers and access to the raw materials of entire moons, they are not anarchists dagnabbit, and they will not put up with everyone hoarding a bunch of whimsical crap or printing out their own flamethrowers whenever they feel like it.

They mostly use rep, unless they're somewhere they need money, in which case they use money. The Ultimates are all about practicality. Among themselves, oddly, I see them as being a little like the Federation in Star Trek in their economic philosophy -- focusing on self-enrichment above all else -- minus the concern for those outside their own faction. They would tend to look down on the accumulation of wealth except as a means to an end. Or, if you like, maybe think of them as being like the feudal Japanese samurai caste, with its total scorn for merchants.