The following SQL queries returned different results:
select count(*)
from site_account where nodehh_idfk1 not in (select pk from nodehh where nodehh_node_id=1501);
and
select count(account_owner_identity_role_idfk1 )
from site_account where nodehh_idfk1 not in (select pk from nodehh where nodehh_node_id=1501);
This issue occurred only on imported tables and only when there was one or more index with the IFIL inulkey member set to 1 (or ctdbGetIndexNullFlag() returned YES for the index).
This problem has been corrected by modifying the ctsqlimp utility so that it skips conditional indexes, temporary indexes (checks already present), and also indexes with c-tree NULL key check activated.