As the title reads I am a bit confused regarding Costume Quest 2 being unavailable on GOG.
We have the first game, and a lot more games by Double Fine, so why not Costume Quest 2?

I imagine Double Fine are most likely to know the answer to that question.

inb4 too niche

Good question, but one you'll probably get no official answer to, so we can only speculate. :/

In many cases it's likely that it has to do with a new publisher, for example:
- while Ittle Dew by Ludosity was self-published and on GOG, Ittle Dew 2 lists Nicalis as new publisher and is Steam only
- while the Tetrobot games by Swing Swing Submarine were self-published and on GOG, Seasons After Fall lists Focus Home entertainment as new publisher and is Steam only
- while Costume Quest by Double Fine was self-published and on GOG, Costume Quest 2 lists Midnight City / Majesco Entertainment as new publisher and is Steam exclusive

But Card City Night 2 by Ludosity is still self-published. So maybe in other cases it's GOG rejecting the titles because previous games didn't sell well or the new one doesn't fully convince them? Or the devs see GOG as not worth the bother anymore?

Those are some valuable observations, and they seem to explain the current situation.