If you plan on making a game using SGDK2 and FMOD and plan on selling it, then yes, it would affect you. You would presumably have to pay the licensing fee based on whether you were selling it on a website or on store shelves. However, you can also use other audio libraries. FMOD is only supplied as a simple solution for the free game developer. For example, DirectSound, while not currently updated, still exists in the latest version of DirectX, and is completely free.
If, on the other hand, your game is being distributed for free, then FMOD is also free to go along with the game. When you start charging for your product, then FMOD starts charging you, and hopefully the sales you make are enough to recoup the sales of the game. I imagine that most if not all SGDK2 games will be distributed freely, at least for now. Later, other sound libraries may be customized to work with SGDK2 as well, so that the user has the choice of which to use. For now, however, FMOD is the only built-in solution because SGDK2's author is not expecting too many games to be built soon with it that will be charging a lot of money for their game.