http://www.inter7.com/courierimap/README.maildirquota.html contains an explanation of how the enhanced maildir standard, or "Maildir++", differs from the original maildir standard. The Courier IMAP homepage mentions that SqWebMail and maildrop also support Maildir++.

Any program that supports Maildir will be able to access directories created by Courier. Programs that use the original Maildir standard will not be able to take advantage of Maildir++ features like multiple folders and subfolders, but messages delivered by the Courier server will still be accessible.

I haven't used mutt, so I may be off-base, but if it conforms to the original Maildir standard, then you shouldn't have any problems. The only inconvenience would be you that you can't access email in folders you created using your IMAP client. Now if the makers of mutt came up with their own way of doing subfolders that doesn't conform to Maildir++, then you're going to have incompatability issues, in that mail moved by mutt can't be read by your IMAP client, and vice versa.

Because of the way Maildir++ defines its heirarchy, and because of the way Courier IMAP differentiates between private and shared mail folders, this is really just an illusion. The inbox is the top-level cur directory; all other mail folders are independent of it. If you use an IMAP client that supports the CAPABILITY command (see http://www.inter7.com/courierimap/FAQ.html#namespace), this becomes more obvious.

Probably because the period is the heirarchy separator.

I believe this was done so that a single directory could be scanned for all relevant mail folders, making it unnecessary to recursively search a directory tree.

My impression is that Courier and its associated programs were designed with remote email services in mind. Even so, it wouldn't be difficult for somebody to come up with a local client that conforms to the Maildir++ standard, just apparently nobody has yet. If this is really an issue for you, your best recourse may be to keep all email in a single folder (cur, the "inbox") that can be read by any Maildir or Maildir++ compatable program.