Essentially I want to know how to get the hidden items that don't appear until later on to... well, appear. For instance the tinymushrooms in mt. moon, and all the items in both underground paths don't appear until you do something. Respectively I believe it is getting cut, rescuing mr. fuji, for the north-south underground path, and beating Giovanni in Silph co.
I don't know if this is 100% true but it's about what I could determine through a recent replay of FRLG. I'm hoping to get a more definite answer, though. There are also spots that are supposed to have hidden items that haven't appeared for me, but I'm not sure how to make it happen. The first I can think of is resort gorgeous. My guess would be needing to beat the elite 4 the second time, which I haven't done yet.