If the conversion away from DirectX is complete, however, some functions may be changed in the code rules. For example, SGDK2 also uses DirectInput, and while you won't be interacting with that for the most part, one place you do interact with it is in the IsKeyPressed function, which takes a Microsoft.DirectX.DirectInput.Key object as the argument.
While I think it would be a good idea to transfer away from DirectX entirely for SGDK2, I'm not entirely certain this will happen, so you needn't worry entirely, and I also think that this won't affect you too much. It should be easy to fix most references to DirectX in the rules.
Also, if you just keep using SGDK2 v2.0, you don't have to worry about anything, because you won't be using OpenGL. The OpenGL system may be an addon that you could import to overwrite the DirectX code, or vice versa, so you can choose which you want to use.
I know that my Weather sample would no longer work with OpenGL unless changes were made, since it draws directly to the screen using DirectX, but if you're not using that, that's not a problem either.