/home/username/mail/user/inbox is no longer used. They were hardlinks to /home/username/mail/domain/user/inbox before, but this was too limiting. An example:
Say there was a user foo who owned a domain bar.com. He created a subdomain foo on bar.com so he now has foo.bar.com. He wanted an e-mail address for both being
blah@bar.com and
blah@foo.bar.com. Previously he couldn't do this since the mailbox in /home/username/mail/user/inbox was used. So only a single one of these addresses could be used, since only one copy of that file can exist. Otherwise they'd both have same inbox. With the current system it is /home/username/mail/domain/user/inbox so each domain or subdomain can have the same users. I hope that makes it clearer.
It should be safe to delete or empty those inboxes, but I would strongly suggest that you run a back up first so you can restore if there are any problems. Thank you very much and please have a wonderful day!