I'm not implying any specific blackmail. I agree, the NSA isn't stupid enough to do that against the President. Our intelligence services certainly have done it against powerful figures, but that's a step too far for any self-serving spy with even a shred of common sense. You don't threaten the President, agreed.
But Obama isn't stupid, either. I doubt they'd need to. You don't need to threaten intelligent people at all, you simply need to make it clear you possess abilities they must consider when planning their actions. The recent admission that they were spying on congress and other government positions seems in line with that. There doesn't need to be blackmail for their power to have an influence over elected officials who might be worried about what they can do. It's not like the individuals in our government are against petty and self-destructive political revenge, and there's been a long-standing run of "official" leaks that just so happen to benefit the organizations doing the leaking, with no consequences for those involved.
But yes, obviously there's also a good chance he has some other reason to continue supporting them. It could just be hubris, the whole pulling together a team of experts to study and advise you on an issue and then almost completely disregarding their reports and deciding things work the way you want. It could be there's a lot of evidence they are combatting terrorism that the publications and leaks simply don't reveal.
Or, as I put as my alternative, it could be the things he thinks he's achieving via them have less to do with terrorism and more to do with some other less-publicized goal. The NSA has had significant involvement in economic espionage at this point as well, haven't they? Certainly seems like there's evidence of a lot more victories there than their is against terrorists.