The Wikimedia clusters contains about 940 wikis (all.dblist contains 934, and the enwiki sites table contains 940).
However, mediawiki_history contains data on only 752 wikis. The missing ones (compared to the sites table) are listed in P8372.
Various types of wikis are excluded, from private coordination wikis (e.g. arbcom_enwiki), to closed content wikis (e.g. akwikibooks), to small, open content wikis (e.g. roa_rupwiki, hiwikivoyage).
All of these wikis should be included; the biggest problem are the missing open content wikis, but even for closed or private wikis we should at least have the data available.