Let's start by separating out Dovecot from Maildir, as it's the Maildir directory structure that you're referring to. It's true that there's no reason to change to Dovecot with DirectAdmin unless you're using Maildir, and so no method to switch to Dovecot exists for keeping mbox mailboxes.
So let's first look at the disadvantage of mbox.
There are two problems with using mbox for email storage. One is that it stores all emails in one file. That file can get very big for users who don't delete email, meaning it can take so long to anything using any of the webmail clients that webmail just doesn't work; it times out. Other issues are that you can run out of space for a user's email if his email quota isn't at least twice the amount of email he's got, because POP and IMAP servers both make a copy of the entire mbox file whenever the user logs in. And that any time an email is deleted from the server, the entire mbox file has to be rewritten.
The second problem is less important; you've probably seen it and ignored it. mbox uses a blank line, followed by a line which begins
(There's a space after the "m") to delimit a new email.
So if an email contains this exact combination of two lines, when it's stored into an mbox mailbox, the transport (in our systems this is done by Exim) adds the
> character in front of the
F in from.
But the first problem is a real problem now that many clients are keeping email on the server and/or using IMAP.
Now that disadvantage you've mentioned concerning Maildir.
Of course you're right, but you shouldn't often have to look at the mailboxes that way.
Maildir was
invented by
Dan Bernstein, who wrote it for machine efficiency, not to make it easy for us humans.
Jeff