For future reference, please put your Zimbra version into your profile. Right now a forum bug makes this a little tricky, but if you refer to the link in my signature you'll see how to do it.
Anyway, with ZCS 6, I believe the default is to use the --zipStore option; see CLI - zmbackup Network Edition Only - Zimbra :: Wiki . So I don't know why your directory structure is unzipped. To verify that there's a hardlink, you can use ls -i on a given subdirectory or file within two full backups. (If it's easier to read you could use ls -il or ls -i1.)
E.g. (partial output):
The number in the first column is the inode; since it's the same, the two directory entries are hardlinked.
ls -i1 full-20111029.080012.959/accounts/a0f/a9b/a0fa9bf3-4176-4434-91b9-c7cb4b52468d/blobs/1/0/
ls -i1 full-20111105.080011.376/accounts/a0f/a9b/a0fa9bf3-4176-4434-91b9-c7cb4b52468d/blobs/1/0/
As for getting --noZip to persist across upgrades, not with ZCS 6, but yes with ZCS 7; see Bug 45634 - add noZip option to zmschedulebackup. However, it's no big deal to just reenter it after each upgrade. The best way is to first do (as zimbra) zmschedulebackup -D to setup the default schedule, then edit the crontab directly with crontab -e. If you don't do this, then not only will the --noZip option be erased, but some of the backup schedule will be gone, too.
WRT setting it in the GUI, they're still working on that: Bug 28199 - Add new zip backup options to admin UI