The goal of replacing the manifolds is to get a freer flowing exhaust system. Freer flowing = more power. Manifolds are definitely more restrictive than OE headers. Oe headers may be slightly more restrictive than aftermarket (looks like smaller diameter tubing)
I am saying by changing from an OEM manifold setup (91-96) to an OEM header setup there are HP gains to be had. I don't know if they are as good as an aftermarket setup, as I have never seen a comparative dyno. However, they are durable and cheaper.
The downside is that you pretty much better plan on swapping out the whole system if you are converting from older to newer. The 3 exhaust sections (header/manifold, cats, cat back/muffler) have varied connection points as Honda changed them over the years. 91-94 has one setup, 95-96 is another and 97 is further changed. There may be differences in the 97+ population that I am not aware of too. Keep in mind you will also have to relocate the O2 sensors, which will likely involve getting extensions to the OE harnesses (from CT maybe?).
SoS has a pretty good visualization of the varying exhaust layouts points I am talking about: (imagine the cats, then manifolds/headers upstream)
Short version
If you find a good deal on a 97+ headers
and cats, it might be a route to consider. You would also have to buy 91-94 to 97 exhaust adapter pipes (SoS sells them) and O2 wiring harness extensions. Power gains would be similar but probably not quite as good as aftermarket.
I think its a bigger hassle than its worth personally, and would just get the CT headers. However, you guys in Cali have a crapload of NSXs so maybe somebody has some laying around and you can save a few bucks.