That's why. 
They'll re-appear if you hold shift (as per the text by the checkbox for that option). Or you can add specific items back, in some cases, as described here. Or have a sub-menu with all the stuff that is hidden, so it's still easy to get to but out of the way.
If you create new items on filetypes you can set their type to Opus-only and that should make them appear in Opus even if the Hide... option is turned on.