No, the GOG version is only the normal game, without the missions, that were part of the SOTY.
It contain some multiplayer and single player missions by the community.
The multiplayer missions were also part of the later released multi-mission-pack by Volition, which is still available in the web and which also get some new voice files that were not present in the Soty.
The single missions were created by the community and so are also still available. Also the two exclusive Demo missions were also part of this package, but lacked the voice files. The Demo Missions were remastered with SCP features and with restored voice files years ago already.
If you use Knossos
for the SCP, there is actually a Pre-Alpha release of my German Retranslation of FreeSpace 2
which includes all Soty Missions next to the restored Demo (yes, it is still playable on english).