The source code for SHOGO has been released from Monolith a long time ago.
Will the source code be available as an extra for SHOGO at GOG?

Good question. I pointed out the Monolith site awhile back which had the full soundtrack and other stuff, including the "source code", so GOG is at least being made aware of "official" material that might make a good addition to the extras. Some care probably needs to be taken, since anything added to the extras becomes "GOG official content" and so could raise support issues that take GOG staffers away from more useful tasks.
As an aside, the term "source code" has been slightly misused by the game industry to refer to the game logic code only rather than the full source code for the game software, engine and all. The game logic source code was primarily targeted to modders, so its value is somewhat limited. It's not enough, for example, to port the game to another platform (eg. Linux, Mac) or to fix bugs that involve the game engine and such. Full source releases, such as id software does for older versions of it's engines/games, are quite rare.