Obama disagrees with some details of the bill, not with the broad outlines. He wants the bill to pass, but he wants some also wants some changes made. He's using (threat of) veto power as leverage to get those changes made. A veto would be a blunt and somewhat counter-productive response, but veto power is the main piece of leverage that comes with the office.
So yeah, he actually likes the bill and the likelihood is that he will sign it or some form of it. The veto threat is just part of the dance.
It's a general strategy, so it applies to the veto threats to both of those bills, as well as a number of others. I think it applies moreso to CISPA than to the NDAA, because my impression is that he has smaller reservations about the details of CISPA.
So yeah, he actually likes the bill and the likelihood is that he will sign it or some form of it. The veto threat is just part of the dance.