These files can be left over from autoexpiry for unknown reasons. They should be deleted depending on age.
One possible reason is if the expire timeout is hit, i.e. when using MailScanner - it can terminate Spamassassin and then the half-processed file stays around. This apparently goes in-hand with growth of the bayes_seen file.
I decided to delete them (found some 500 day olds on the servers I took over) and to only delete those that are most probably not in use by anything.
The full solution is of course to let it not timeout, still searching for this.