Didn't know GOG had Prophecy until I saw the Wing Commander Series sale today.. It's interesting how much one loathes putting in CDs and even switching them in this day and age..
I can confirm that it's still using a Glide Wrapper and is not using the OpenGL patch available from CIC (and neither does it deliver the DVD movies, but those haven't ever been officially released anyway).
You can apply the OpenGL patch though and the game seems to work without problems so far.
For those not in the know:
The OpenGL patch is much more advanced than the Glide Wrapper (the wrapper presents the game "the way it was" using the Glide graphics API) as it patches/changes texture information, replaces some textures, allows for Anti-Aliasing and Anisotropic Filtering and upscales all 2D elements smoothly (the Glide wrapper's scaling is quite crude).
It might have been nice of GOG to have that patch pre-applied but I can imagine that the legal situation doesn't allow it (the patch's authors retain rights for the changes they made, e.g. new textures, while infringing on other rights, e.g. "patching" the libraries and executables).