autovacuum_naptime being only 5 seconds seems too frequent. A lock_timeout might be 1-5 seconds depending on your system. Usually, DDL can fail and wait a little time rather than lock the table for minutes and have all reads back up behind the DDL.
Given you have autovacuum_vacuum_cost_limit set to unlimited (seems very odd), I'm not sure a manual vacuum freeze command on the tables with high age would perform differently. Still, issuing a vacuum freeze and then killing the autovacuum process might be worth trying.
