I know GOG works on the games to get them to work on newer hardware and OSs, but what about new input hardware, such as the X52 pro. I read a little about on the Hard Light forums about people getting their X52s and X52 Pros working with the game, but no matter what I seem to do the games will not detect my button presses or axis movements.

Does anyone have suggestions?

Hmmm ... Have you tried installing the Freespace Open Engine? That's typically what people are using on the hard-light forums (though they do discuss Freespace 1/2 vanilla there too). This person on GOG uses an X52 and got it working in Freespace 2 with the Freespace Open Engine:

http://www.gog.com/en/forum/freespace_series/playing_freespace_2_on_an_x52_without_profiles