Reading the Maildir documentation they just mention folder should be like
user/Maildir/cur
tmp
new
So my virtual users have it without Maildir folder like:
user/cur
/tmp
/new
is this going to cause any trouble in the future? Or is this a wrong way to use it?
I think it mostly a historical convention which assumes that users have an actual home directory and more access than just to their e-mail. Then it makes sense to have a ~/Maildir/ subdirectory in addition to ~/public_html/ , ~/.ssh/ etc.
For virtual mail users there isn't much actual need for such an intermediate ~/Maildir/ directory, but using it doesn't incur much cost (1 inode per mail user) and changing it will require explicit configuration in most software (if possible at all), possibly resulting in portability issues when migrating to a different mail system in the future.
Typically I'm strongly in favour of doing the conventional and I would recommend sticking with the ~/Maildir/. Just because you can change from the defaults doesn't mean you should.
I have my own experience with this setup because I'm using dovecot without a ~/Maildir/ subdirectory. It's usually no problem at all, the only thing I noticed is that users can under certain circumstances see system folders in their mail client. In my case, users keep asking me what the 'dovecot' and 'sieve' folders in the folder subscription windows are for...
To avoid such artifacts, I'd suggest to stick with the ~/Maildir/-setup. This way you can keep a clear separation between mail folders and configuration stuff.
