You can be certain that Volition and Interplay did not allow the game to be sold out of the kindness of their own hearts, I'm not privy to their legal department, so I cannot say whether the royalties are per-unit or time based, but the length of time it's been on GoG implies a per-unit arrangement, so just because they are not selling the product, do not be so certain they are not profiting from the sales.
As for 'preventing FS3 from being made', I applaud your sense of the dramatic, but it's far, far more than the fact that a third party is distributing the original game that is preventing FS3 from appearing.