Shelving locations that are setup in the LOC category allow libraries to include a location or not, based on whether they use the location in cataloging. This makes sense. What cataloger wants to sift through a bunch of shelving locations they are never going to use? However, if you allow advanced searching to use shelving locations as a limiter (AdvancedSearchTypes), if you are on the staff client in advance search, you have the same locations restricted imposed on search.pl, which is not what one would want. Staff will never be able to limit to a shelving location used at another library. I don't think that the library limitations in LOC should apply to search.pl.
IIRC this behavior dates back to when the feature of library limitations for shelving locations and collections was added, but I always found it not very useful. Something that makes sense for making things easier for catalogers in the library, doesn't necessarily affect patrons in the same way - meaning that they could still order/use items from all libraries. I'd love if we made this configurable, as it can prevent the use of library limitations for some libraries currently.