Wondering what anyone thinks about this idea; if it sounds reasonable. I'm looking at a system where you can use your cellphone to ask for help from the "Master" who set all these puzzles.

There's an (unreachable) room called "hints box", filled with hints. Each hint is an object. They have properties "enabled" and "solved". For example, if you try to open the red door and get the "it's locked" messagem the hint about finding the red key becomes enabled.

You can then "ask for help with #text#" or "ask for help". Both pick an enabled hint from the hints box, and put it in your phone where you can read it. The one where you specify a subject filters the pool of hints before choosing one.

Once you open the door, that hint is obviously no use. I was wondering what I should do with them; just delete them? Or maybe hints for solved problems become edible :p It sounds silly, but might work. I'm wondering if that feels fair; or what kind of bonus they could give when eaten.

Also unsure about the wording of the commands. It feels unintuitive, but I don't know what would be better. Any suggestions?

It depends upon your game design: you can certainly use Objects, removing or destroying them, and/or you can use List Attributes and/or Dictionary Attributes, adding/removing them.

That sounds reasonable.

On one of my (unpublished) games, I filled a room with "personified" questions. What I mean is, I named the objects on a variety of topics, combat, healing, Pokémon itself, etc. It's not too different from what you are thinking.