The logs folder is used for the various log files and it is a root/root (owner/group) file so you would need to contact support. The Maildir folder is username/group so could be re created but I am not sure if the sub-folders under that would be recreated.
Unless you have started to put data into the sub-domain then probably the best bet would be to delete the sub-domain via the Control Panel (maybe check via ssh/ftp that all traces have gone) then after a suitable time re-create your sub-domain again and the happy domain robot should put those folders back in place.
If your domain name is missing those folders as well then it is time to contact support. (If you created the new domain yourself from your already installed account you could of course delete the lot via the Control Panel and start again. Just make sure that they are deleted because I have had some not delete properly.)