A permanent retention policy wasn't, apparently, the reason ONRL has those logs, as those records are identified as “records acquired from private citizens”. [0]
Yes, the permanent retention policy came well after the days of the Continental Navy.
Those requirements are currently set out in SECNAV M-5210.1. Nowadays, they're maintained by NAVHISTHERITAGECOM and then transferred to the National Archives after 30-years.
[0] https://www.archives.gov/research/guide-fed-records/groups/0...