Currently can't find any way other than brute force and manually going through the files to remove old and unused player data. I've got 38 thousand user data .yml files and would like to clean them up somehow..

It's a bit hidden. Use /essentials cleanup <days> [money] [homes], where days is the time that has to have passed for purge since last login, and you can define exemptions for players who have more than x money/homes.

Does it work for mail? or to even purge the entire userdata file if the player hasn't been on for more than 100 days?

This will clear the whole userdata file of affected players. That includes mails.

On this issue tracker aswell, don't expect it to be implemented though. There are tons of feature requests already.

Thank you :)

Thank you for your help, one last question, where could I request a feature?