Many of the POIs and goals that NOA might give you are fully bypassed if you’ve already found them (perhaps due to ignoring the NOA alerts for a very long time).
NOA should send all of these alerts anyway.
It may not make sense for NOA to ask you to investigate a black box that you already found, but if you are not given these goals, then the resulting beacon location is a “missable” entry.
Let’s not hassle our extremely OCD players in this way. Give the expected beacons and dialog lines no matter what.