Currently, there is no way to hide a whole Collection code from the OPAC. A library can hide items in a collection, but this Collection Code will still appear on the Advanced Search page. It would be nice to add the ability to hide entire Collection codes through the Authorized Value setup of the Collection codes itself.
Or maybe a syspref that lets one list ccode to hide from the search interface? This is a nice parallel to what we do with item types, but that's a bit different as they have their own table with a column to hold this setting. I'd suggest that whatever we do for ccodes, we should also do for shelving locations.