The Humble Bundle version was last updated on August 12, and that's when the multiplayer version was merged with the regular version. So if the latest GOG version is significantly older than that I guess the GOG version might not have multiplayer. But surely that can't be the case, can it?
One change from the initial Steam multiplayer version was that instead of choosing to join a multiplayer game in the menu for loading saved games, there's now a mandatory choice between singleplayer and multiplayer before even getting to that menu. So in that latest version there should be no question if it's available or not.
EDIT: "Changelog for Patch 1.13.02/ GOG-11 (Windows)/ GOG-9 (Linux and Mac) (added 15 July 2016)" should mean that multiplayer is available, since that was initially introduced in 1.10.00. Steam and Humble Bundle are up to 1.13.06 though, which is one patch ahead. And checking my 1.13.02 version, it has the "Singleplayer" or "Multiplayer-beta" option right after the "user login" screen.
Are your games updated? Or do you expect to be able to "Join Multiplayer"? That won't work very well with 1.13.02, since everyone else has updated to 1.13.06, and also password-protected their games so they can play through the campaign with people of their choosing, rather than some random internet stranger who won't be around for the next session. I used to sometimes host an open multiplayer game, and sometimes others would join for a bit of mayhem. But I've finally gotten around to playing some other games now, so I don't do that anymore.
Post edited November 29, 2016 by Gillsing