If you have the Hide low SOL contacts in 3D option on, you won't see contacts in the 3D view unless you have an accurate firing solution on them.
I'm guessing what you're experiencing is a combination of that and not using the periscope's laser designation function (I).
If that's the case, the devs should still probably look into the matter and allow all contacts to be seen through the periscope: I don't think it's a good idea to have anything artificially hidden from your only "legitimate" visual sensor.
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