Alright, I did what you suggested:
In qa-db-post-create.php I changed line 333 from:
qa_db_query_sub("REPLACE ^options (title, content) SELECT 'cache_unaqcount', COUNT(*) FROM ^posts WHERE type='Q' AND acount=0");
to:
qa_db_query_sub("REPLACE ^options (title, content) SELECT 'cache_unaqcount', COUNT(*) FROM ^posts WHERE type='Q' AND acount=0 AND closedbyid IS NULL");
Then I clicked >Admin >Stats >Recount Posts. Now the pagination is correct.
I only hope that this is not causing any other statistics / routines to break or count false...