As Shadow said there's a limit of 300 titles that can be displayed on the system menu at once. You can use an alternate launcher to launch the titles that are beyond the 300 limit, but I assume you have a lot of VC titles installed, the better option would be to simply use homebrew emulators instead of VC. With the exception of GBA (and maybe SNES), they are better than the VC ones anyway.
Have you checked all the pages to make sure you didn't just miss them?
Can you launch them through FBI->Titles?
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