I think having quests in secret areas is totally fine, they just needs a hint like "look for a hidden door in the jungle bar" to narrow down the search. You could even have an NPC in the same area comment on seeing a hidden door near the flying saucer or something of the sort.
I don't know much about GameMaker but I don't think you need to keep track of every NPC. A simple way might be just to check the sprite file they're using and then use that file name to find the corresponding entry in the guest book. That way you wouldn't need to change a single thing about any of the characters on the map or give assign them any additional data. The game would automatically know which characters match and which don't. It would also detect transformed characters since they're now using a different sprite.
Definitely looking forward to seeing what you make for Strawberry Jam. Howling Good was one of my absolute favorite submissions in last year's event.