Are Custom Profile Fields supported when doing Site User Imports or Exports?

Yes. If you have Custom Profile Fields setup on your site, those can be included when doing site user imports or exports to your site.
When downloading the site user records from User Management > Site Users > gear icon dropdown menu at the top of the listing > Import/Export Users and choosing either Download Excel Template or Export Now. But only Custom Profile Fields that are set to Show on Form on User Management > Profile Fields will be included in those exports.
You may need to set all your custom profile fields to Show On Form when downloading a site user list to import back to the site when populating the users, and then setting any that should not show to your users to have Show on Form disabled while preparing your site users.