According to this page, the items in the Underground Path on Routes 5-6 do not appear until you have visited the S.S. Anne. However, this page claims that all but one of the items in the Underground Path on Routes 5-6 do not appear until you obtain the Vs. Seeker from the Pokémon Center in Vermillion City.
Both pages agree that all but one of the items in the Underground Path on Routes 7-8 don't appear until you clear the Rocket Warehouse.
I would try what each page suggests and then see if the items appear.
Neither site mentions anything about items in Mt. Moon not appearing, so they should be there. You might've collected them already or you could be looking in the wrong locations.