Obviously Meta still has rep, it's just hidden. I'd call this a bug though since I was notified of it and it shows up in my activity and so on, which is not exactly hidden.
This is status-bydesign. From Jeff on Should I really have been awarded mortarboard on a Per-site meta?:
Just redefine it as "you received a lot of upvotes in a single day". So I think it is correct in spirit.