Short answer: Yes, they will require a merge, and yes, they are being merged.
Long answer: For a brief interval, I had also had two accounts: my old Chiphacker mod/user account, as well as an Area51 account, so I merged the two. There weren't any other dupes that I noticed at the time, because the duplicate account isn't created until you log in with the 2.0 account (We might be dealing with this for some time), and I did this within a few minutes after the site opened. Ideally, this would become an automated thing (if it's not already).
Yes, it can and will be done. However, mod resources are stretched right now. On both SE 1.0 and SE 2.0, moderators and administrators can merge accounts. On Chiphacker, everyone with over 2.5k rep was a moderator, along with a few other notable contributors, plus the admins littlebirdceo and mad_z, so things happened pretty fast.
Now, reputation gets you the privileges described here, the highest of which is a subset of the privileges afforded to a moderator. The privileges afforded to a user with 2,000 rep described in the link consist of everything listed there, the right to see (and undelete) deleted posts, as well as access to these moderation tools (lists of ___):
- posts flagged as offensive or spam
- recently deleted posts
- recently closed questions
- see all recent edits in chronological order
- new posts by new users
- questions with newly created tags
- new answers to old questions
- recent questions with most view velocity
- recent questions with most edit velocity
- recent questions with most vote velocity
Everything else has to be taken care of by someone from Stack Overflow Internet Services, inc. At the present time, that includes Jarrod Dixon, Jeff Atwood, Jin, David Fullerton, Geoff Dalgas, and Robert Cartaino (Denoted by a ♦ by their username). In the future, we can elect moderators from our own ranks.