Hi,
At least on the Breton Wikisource, the special page PagesWithoutScans ( https://br.wikisource.org/wiki/Dibar:PagesWithoutScans ) doesn't take the magicword __DISAMBIG__ into account.
There should be only 17 pages for there is 176 pages right now (the 17 pages + 159 disambiguation pages)
Cheers
from enWS perspective, couldn't tell you, we well hit the 5000 limit well before disambiguation pages
On vec.wikisource, which has a small number of pages, PagesWithoutScans correctly doesn't show disambiguation pages.
So this seems to be more of a configuration problem.
The special page tries to exclude disambig pages, first by looking into Mediawiki:Proofreadpage-disambiguationspage, which should contain the pagename of the disambiguation template (only one); if this is not found, it looks into Mediawiki:Disambiguationspage, which should contain a list of all disambiguation templates.
On br.source, the first one points to a non-existing template, the second is empty.
Can you try to set either one of these two messages and see if this solves the problem?
Closing at resolved, as it was a configuration issue related to br.source only, and it seems to have been solved.