When you're doing it in 1964, it's different. You not only press Ctrl+C to open the GameShark cheats dialoge in 1964 and then type the cheats by their codes that you want to import, but you also have to select the cheats and click the "Select" button at the bottom-left.
If you already did that, then Idk. To be honest, I've found cheats in 1964 that didn't do anything, either. Try copying and pasting the cheats from Project64 and use them on 1964, and then they should work. For some reason, the cheats for Zelda OOT on 1964 indeed seem ineffective.