Okay so I believe I know the answer to this but I am just making sure.

When a hero is exhausted, and someone plays Naith Guide, can they choose the already exhausted hero as the target?

I don't think so as I think the hero needs to be ready to commit to the quest, even if they don't have to exhaust for it. I just want confirmation, though.

No they can't

Technically, you can choose the hero, but without some additional way of readying the hero, you can't get any benefit.