And since most of STAR TREK takes place out on the Final Frontier, on strange new worlds light-years away from the Federation, it probably doesn't really matter much. If your plot needs money, just set it on a distant world or colony where the alien inhabitants still use money. It only becomes an issue if you have a Starfleet officer or Federation bureaucrat scheming to get rich for some reason, which would be problematic. (Unless they're also planning to set themselves up as rich expatriates on some less civilized world.)
Personally, I've managed to write nearly twenty STAR TREK adventures without having to deal with the topic at all. Like I said before, the nuts-and-bolts of the Federation's economy really doesn't matter when a landing party is beaming down to Zyzon Gamma VI or encountering a mysterious alien probe in deep space . . . .
