Just what the thread subject asks: Will the GOG version of Mark Of The Ninja Special Edition Upgrade work with the Humble Bundle release of the base game?

No. All game upgrades sold on GOG require you to have the base game in your library. If you don't, though you can still purchase an upgrade, it sits idly on you game shelf, since all it does is unlock updates to your GOG in-library copy of the game.

Oh, I see how it works. Basically, the purchaser is buying an unlocker.

Thank you for the info!