Yep, my Micra DIG-S is a manual and I do know the Note's over here also came with both boxes. They perform ok I suppose but are far punchier than a CVT just simply down to the fact of the operating differences.
I am not aware of any particular problems with the manual and ours now has 85k miles.
Due to the cost and potential complexity of swapping a CVT to a manual, most people will just either refurb/replace like for like, or just get rid.