I think all resolved signals should still show a spike in the frequency spectrum, refer to my posted image, that was a resolved signal, and yes it did also show up in the nav panel, but it still shows in the frequency spectrum. I'm not sure about USS's because they do time out and vanish so maybe they are different.
I think what's happened to me a few times is that I had a scenario present when I did the honk, but by the time I got around to hunting for it the timer had run down and it went away. The blip still showed on my spectrograph even though the scenario had seemingly vanished. I have found a few too when they were still active, but when they did run down and fade I still had a blip on the spectrograph, but the (1) symbol beneath it had vanished.