They are not disregarded but they are not guaranteed to be current with the group's permissions. Furthermore the group's permissions are currently, as I've already mentioned, authoritative for all objects belonging that group. Keeping permissions in sync would at present require the update of potentially millions of rows upon a group permission change. We have not removed the columns (
http://trac.openmicroscopy.org.uk/ome/ticket/2580) due to their potential to be used in the future or even kept in sync with the group in the future.
Fundamentally the database schema is not a public API. Performing operations directly (ie. in SQL) on the database is completely unsupported by the OME team except in very specific cases.