Will we be getting the D3D Megaton Edition here on Gog?

Only the GOG Team would be able to answer that. As far as I know, they haven't said anything about it.

I will say this: The wishlist isn't marked as In Progress. None of the wishlists for the Atomic Edition add-ons are marked as In Progress either.

It should probably be worth mentioning that the Megaton Edition uses Steamworks for the multiplayer. That said, I highly doubt this setting foot outside of Steam. Without that it's pretty much DN3D on an extremely old version of Eduke32 without need to hunt for expansions.

I would love to see the expansions themselves on GOG though.

When the game was released, the creators confirmed once that Megaton Edition will NOT come to GOG any time in the foreseeable future.