It would appear that at this time of writing, the regular edition of Age of Wonders III has been pulled from GOG.
I could not be sure of the reason for this, but I have seen the user reviews for the regular edition - most of them were not kind and mentioned the presence of DRM in the game.
The common complaint among them though is that what they were promised was not in the GOG package for the game, but rather on some other distribution channel.
There is that, and that the deluxe version is still there.
I personally doubt that Triumph Studios did this - it is more likely that GOG itself did, possibly after many (very likely) complaints and demands for refunds. (GOG has a 30-day refund guarantee, remember?)
UPDATE: It appears to be back, half a day later. I do not know what has changed.
UPDATE #2: And it's gone again, at this time of writing.