Could I offer our reasoning for choosing Maildir?
I made the decision that we would use Maildir because I was worried about the effect of loss of a single file. As I understood it, mbox stores all the messages in single file and, if the file was corrupted and couldn't be recovered for any reason, then we'd lost a whole lot of messages. I do not agree to this view; there are two possible scenarios what could happen:
a) filesystem corruption - with maildir you probably end up with an ugly mess of unconnected directories, while for mbox you need to find the one file (per folder) for user x.
b) file is corrupt (altered by two processes, bad sector, filesystem corruption on file level) - the mbox file can be repaired easily, if you want, by hand. For maildir you need to find the affected parts of the directory structure, probably more than one file will be affected as dovecot needs to open many nodes simultaneously
In all these cases it is best to have a current backup (which is easy to say but hard to achieve with classical backup methods for a mail folder). In either case you could spend hours on fitting pieces together and even then you are not sure that nothing is missing.
That said, we use maildir and mbox formats for several hundred mailaccounts in different setups and never had a real corruption problem, besides one issue with badly formatted From: lines several years ago.
Jakob Curdes