I don't think there being two there explains anything at all. The connector looks like it has about 40 pins in it, two rows of 20. The '95 Hardbody that I used to own had far more pins than that to its relatively simple ECM under the seat, and the connectors were not shaped quite like that either. Granted there were a lot of changes for the debut of the '98 Frontier, but since it was an evolutionary design instead of a clean-sheet design I doubt that it would have been that extreme of a change. Additionally if the ECM had been abandoned in-place and a second one bolted in, there wouldn't be a harness connector unhooked, it would be plugged into the replacement ECM.
What I see that makes me wonder is a second harness connected further along the housing, looking like it's got one or two wires in it with some fairly thick shielding. I think it looks like an antenna wire of some kind, which combined with the number of pins in the unhooked connector makes me think this has something to do with the entertainment system, like a satellite receiver of some kind. If the truck is so equipped and the previous owner stopped subscribing then perhaps this was a way to disable it so the main radio wouldn't keep presenting satellite radio as an option when switching through the bands.
It would be really helpful to know the year, cab configuration, and trim level though, otherwise we're guessing at what it is.