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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.

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I had the exact same problem when I could not find the TinyMushrooms in Mt. Moon after starting a new game and I could not find an explanation anywhere on the internet.

I started asking questions around and someone finally helped me on the Pokecommunity. Here is the link, Basically it says that hidden items can be set dynamically, so there is an in-game event that sets the ability of picking them up. This event can really be anything, for example:

  • Acquiring Cut or the second Gym Badge
  • Traveling through Diglett Tunnel

Maybe we can find out in the future for all hidden items. It baffles me that after almost 15 years (!!!) we still don't know when the hidden items spawn in two of the most played games on the Game Boy Advance. It's too ridiculous to be true, but, it is true. No one knows it.

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Bulbapedia provides a nice wiki on the hidden items.

Other hidden items, such as Poké Balls, valuable items, and medicine, also recur in various areas around Kanto. In each area that has recurring items, there are three different item "groups": common (A), uncommon (B), and rare (C). At the beginning of the game, all of these spots are empty; after every 1500 steps the player takes, when they next visit any area with recurring items, the recurring items in every area in the game will be refreshed. This deletes any recurring items that the player has not yet picked up. Then, for each area, the game randomly selects one of the three item groups (each having a different probability). Every item in the chosen group will be spawned in the area; if the chosen group is empty, nothing will spawn.


                               Group A  Group B                           Group C                             
Mt Moon (B1F)                  (Empty)  3x Tiny Mushroom                  3x Tiny Mushroom | 3x Big Mushroom  
Underground Path (Routes 5-6)  (Empty)  Potion | Antidote | Parlyz Heal   Ether                               
Underground Path (Routes 7-8)  (Empty)  Awakening | Burn Heal | Ice Heal  Ether                               

https://bulbapedia.bulbagarden.net/wiki/Recurring_item#Generation_III

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