Clearance issues. Cost vs benefit issues. I have never seen aftermarket headers targeted at hemi conversions. Maybe they exist, but I doubt it.
The clearance issues are numerous. Its so tight that on 2011 (I think, maybe 2010) and newer hemi's AEV's kit requires you to replace the exhaust manifolds with the old style "log" ones that were used on hemis from 2005(?) thru 2010. (I may be off a year on either end.) Now, I have seen people maintain the factory exhaust manifolds on the 5.7 vvt motors and even a couple that have kept the 6.4 vvt manifolds. But doing so requires some trimming, fitting and creative custom exhaust work. And let's not forget that you need cats on the exhaust and you need them as close to the exhaust ports as possible so they achieve the required temperature to function correctly. (This of course assumes you need to pass a real smog test.)
Interference with aftermarket lifts, control arms and skids has to be factored in as well.
In the end, I think it is more cost effective to maintain the factory 5.7 vvt or the 6.4 exhaust manifolds. From what I have read, the 6.4 manifolds flow pretty damn well. I think doing that would get you 90% of what headers would get at substantially less cost. Thus the cost vs benefit part. Not to mention that adding headers may impact other areas of the performance envelope. And given the limited aftermarket support in general of the hemi motors, I don't think many people have the desire to go blindly into something like headers on a JK conversion. While not likely, it is possible you could actually do more harm than good. You may need a cam change to take full advantage of the headers. And changing the cam in a hemi is no small expense. One thing leads to another.........where does it end?