Said with aftermarket headers it will prevent the head from cracking, stock manifolds are causing the cracking.
I wouldn't say that's the full cause of the problem; given a 2.9L with the older heads, they can last as long as the engine doesn't over heat. Some crack without ever seeing signs of over heating. But it could contribute to the problem.
It seems that the culprit of head cracking is unmaintained cooling systems and poor casting/design from Ford. I would suspect that switching over to headers wouldn't fully prevent this from happening, really the only 'fix' is better casted heads (eg. World Products) if you have a cracked head. And if you haven't cracked one yet, make sure the cooling system is free of leaks, coolant is fresh, and that it's in good working order.
IMO, best thing you could do to monitor your cooling system is to install an aftermarket temperature gauge.
FWIW, It's likely that in the event of installing the headers, the exhaust bolts will snap off into the heads. I am not sure if that's something you'd like to get into...
I don't want to discourage you from this

, if you want headers, do it. And I agree, headers will help with venting some heat, but I am not sure that's going to help much when the head itself is the flaw. Exhaust is going to get hot as hell no matter what.
Pete
Edit:
Side note, and the heads always tend to crack on the #1 and #6 cylinders. The heads are interchangeable from left to right, #1 and #6 are the same cylinders. To me, IMO, this sort of debunks the possibility that the manifold is the main cause of it.