As for ROM ripping tools, you're assuming that Nintendo took someone else's non-commercial ROM ripping tool and used it, instead of dumping the ROM themselves. Besides, where do you even get the info that "every ROM ripping tool" is for Non-commercial purposes? I just searched for a NSES rom dumper and found something called the Kazzo cartridge "INL Retro" NES Dumper-Programmer and there's no sign anywhere on the page or the readme.txt of it being restricted to non-commercial purposes.
> Source: I own patents
Then you should know that you actually have to file for patents in order to have them, which the author of the iNES format didn't do (and couldn't even do, because there's nothing in there that qualifies for patent protection).
In my interpretation the bytes in the file are just a description of facts, and it is highly unlikely that the act of writing down facts about the cartridge in a specific way is enough to create a work on its own that could be protected. Calling them "code" IMHO would be quite misleading, since that would lead to confusion with a program or the executable code in the image. (Larger data sets/ROM collections might be protectable under database copyright laws in jurisdictions where those exist)
Just to be sure: If you mean a software implementation reading/writing said header, that of course could have copyright protection.
> By the way, every ROM ripping tool explicitly states "Non-commercial purposes"
There are open-source (BSD licensed) tools that have no such limitations.
And if nobody can own a file format, please explain Adobe's patent on the PSD or DNG formats themselves (owning the specification = owning the format.)
“Essential Claim” means a claim of a patent, whenever and wherever issued, that Adobe has the right to license without payment of royalty or other fee that is unavoidably infringed by implementation of the DNG Specification (from https://helpx.adobe.com/photoshop/digital-negative.html#dng)
The patents are not on the file format, but cover techniques required to implement an application reading it. Similar to how you have to pay to use e.g. MPEG4, since various companies have patented parts of the compression mechanisms. The patents don't cover just MPEG4, but any video format using these mechanisms.
By the way, every ROM ripping tool explicitly states "Non-commercial purposes" so Nintendo still violates a specific licensing limitation by using a ROM made using those tools, whether they own the property or not. Any way you try twisting this argument, you're going to lose, hard.
Source: I own patents, have successfully defended my IP in court, and I actually read those little things that nobody else apparently does that LEGALLY puts restrictions upon the software use.