The drawback is that if users do ctrl-F to find a term and don't realize that they're only seeing part of the finding aid, they may miss something.
It depends on what powers your general website searching, but I solved this by having a special "Search this finding aid" page that constructs a search specific to the finding aid in question. Not quite a Ctrl-F, but leads them to a page where they can do Ctrl-F.
@Ethan Gruber: I'm curious how EADitor handles very large finding aids (back- or front-end). Are there XML/XSLT/XFORMS solutions that haven't yet been discussed here?