Is it just me or does anybody else realize that Shadow Moses Island, Skyward Voyage, and Silph Co. are missing? What happened? Are they unlockable now? Permanently removed?

They're not unlockable; they don't exist in the game's files right now. So the only possibilities left are:
1. that they're being repaired/reworked and will be added in a future auto-update, like Venus Lighthouse is confirmed to be, or
2. that they were cut entirely due to lack of popularity or some other factor.
And the developers are refusing to answer which; several people have tried asking already. So we'll just have to wait and see.