If the Dark Lord allowed to Denethor to see only what He wanted to see, then I don't think Denethor ever learnt that Aragorn had the Orthanc Stone, unless he saw it in Pippin, who himself didn't know who had it (Gndalf gave it to Aragorn in secret). Pippin shortly refers to Aragorn in front of Beregond without stressing much; maybe Beregond gave this away to Denethor.
As for Aragorn not raising the standard, maybe he had it raised from Pelargir but Denethor couldn't see enough detail to notice it (or he was too desperate to pay attention). On the other hand, we don't know for sure wether Aragorn knew that Denethor had a Stone or not. He certainly wasn't expecting him to be watching.
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