I doubt they're still making prints of FFC, seeing how they no longer make new prints of their PSX games (if i do recall correctly). All the money just goes to the distributers and various other (internet) third-parties now, not the producers...
But, in a way, I think it still does...CT (and RD & CC, mind you) kicks ass, and thusly gives a good name to Square(-Enix) and so people will try their other games because they have played an asskicking game of theirs.
Also, it was a merger. Enix didn't 'buy them out'. As I recall, Square was just getting out of their Spirits Within whole when they released FFX and such...Nothing 'happened' to Squaresoft...Although some of the talent went freelance...They've still got a lot more opprotunity now that they're merged with the Japanese powerhouse of Enix. If they ever decide to do an actual RPG Dragon Quest (Warrior)/Final Fantasy cross-over, the world will explode.