Ray-
Not checkboxes, which would indeed require so many that they would become rigid and/or useless. I would propose searchable write-in boxes where words and/or codes could be entered.
This sounds a lot like my proposed [[Category:Foo]] scheme, only that you want codes instead of words for the categories. My scheme has the advantage that it can be built very easily on top of the existing data structures, with no extra input fields or changes to RC required.
With this scheme, you would have
[[Category:Sex]] [[Category:Sexually explicit]] or [[Category:Religion]] or [[Category:Music]]
and meta-categories:
[[Category:Stub]] or [[Category:Delete]] or [[Category:NPOV dispute]]
each of these category pages would be editable, but always automatically include a sorted list of the pages that link to the category ("what links here"). It would also be nice if a text could be configured for each category that is displayed on pages that are part of it, e.g.
[[Category:Stub]] -> This article is a stub article ...
Regards,
Erik