Disclaimer: I've never (yet) run headers on a 40, but I've installed and run them on lots of other vehicles, including a 3FE-powered FJ80, so these observations are only my experience with headers in general:
1. Without other engine mods (induction upgrades, more aggressive cam, higher compression, etc.) headers by themselves will do little or nothing to improve performance. They usually make things simpler and less complex though; not a bad thing in and of itself.
2. Every set of headers I've ever had eventually rusted out from the inside. Ceramic and other specialty coatings can delay the inevitable, but in the end rust still wins. Ergo, headers are not a permanent fixture, you might have to replace them if you're keeping your truck for a long time. Stock manifolds rust too, but thick cast iron takes longer than the life of the truck to rust through. The thickness of the steel tubing in headers is miniscule compared to the thickness of a cast-iron manifold.
3. Because of the thinner material and the vastly greater surface area of headers, they radiate a LOT of heat into everything nearby - the engine compartment and the firewall (and hence the cab and floorboards) for example. Heat in the engine compartment tends to bake vacuum lines and plastic parts to brittleness. You can mitigate this somewhat by wrapping the headers but this encourages rust from the outside as well as the inside.
I'm not against headers, like I said I've used them a lot on many vehicles. You just need to be aware of the trade-offs for running them to make an informed decision on whether to install them or not.