There are several things that can be the culprit. Wire harness itself is pretty low on the list.
If the "BRAKE LAMP" warning on the safety indicator is intermittently turning on and off, do you have any other symptoms of things being "odd" in respect to how electrical components in the trunk are functioning? Most notable, does the power antenna still extend and retract at normal speed or is it slow/"jerky"? Also, are you running the incandescent bulbs (standard) or do you have LED brake lights installed?
How I would go about this:
1) Familiarize yourself with the information and troubleshooting regarding this indication in the Factory Service Manual. It will be in Chapter 23.
2) Check the brake lights themselves - are any burned out? Do any have corrosion on the base?
3) Look at the condition of the bulb sockets while checking the bulbs. Since bulbs are cheap, I would just put a new set of bulbs (all 4 of them) in while I've got the tail lights accessed.
4) Check the connectors (I would recommend disconnecting the various connectors in the trunk (there are ones at the tail lights themselves, and then there is a large connector in the front left corner of the trunk behind the lining), clean them with some QD Electronic Cleaner spray then make them back up.
5) Have somebody follow you and see if the tail lights/brake lights are flickering as the car goes over bumps. And if they note they are flickering, is the "BRAKE LAMP" warning also flickering on/off?
6) Check the trunk ground (G551) - it is on the left side (you need to remove the trunk side liner that has the light in it) and it is by the power antenna motor. If that is loose, then you could get flickering lights, sluggish/"jerky" antenna operation, and the "BRAKE LAMP" warning on.
Now, if the tail light/brake light bulbs are good, and there isn't any noticeable issues with the wire harness, then do the troubleshooting of the lamp failure detection modules (again, in Chapter 23 of the NSX Factory Service Manaul)
Finally, keep in mind that the "BRAKE LAMP" warning coming on when the bulbs and detection modules are good is a "leading indicator" for leaking capacitors in the instrument cluster itself. If everything checks out, I recommend removing the instrument cluster and opening it up to see if there is any leaking capacitors in the instrument cluster. Instrument Cluster removal is detailed in Chapter 23 as well. If you are careful and use the tilt/telescope features of the steering column to your advantage, you can remove the instrument cluster without having to remove the steering column covers like the removal procedure calls for. Even if you don't find any significant issues with the capacitors, I recommend boxing up the instrument cluster and sending it to Brian Kiehnau at nsxe-repair and have him replace the capacitors with new, modern capacitors. Leaking capacitors in the instrument cluster have been linked to at least two or three electrical fires that have causes significant damage (in one case, I think the affected NSX was a total loss)
But don't think the system "fixed itself" if the indication was on and suddnely turns off by itself.