Does the GOG version contain the secret mission at the end?

I dont know, yet, Im not there. But I will let you know when I've completed it - only a few missions left I think.

Playing the game at the moment and really enjoying it - highly recommend.

Yep it sure does!

I completed the game tonight and then was able to select the Secret Mission.

So no reason not to get the GOG version and start snipping away!

What a great game - loved it!