Technically Master Xehanort hadn't seen Sora until Kingdom Hearts, as he was Ansem at the time. The most likely reason for him not caring is he likely believed Vanitas had merely become his own person or just looked like nobody else, he didn't know about Ven's heart having been joined with Sora's.
Even then, all Reports that were written by Xehanort were done so
before KH I. The only reports that cover the time of KH 1, CoM and part of KH 2 are the secret Ansem Reports from KH2 which were written by Ansem the Wise.
Vanitas' "Sora"-face was seen by only two people ever, those being Master Xehanort (the old dude who never saw Sora until DDD) and Ventus.
I also wouldn't put it past MX to have acknowledged their resemblance in his mind, but not show any signs of fascination or confusion until writing it down in a report. If there's any character in the series smart enough to put two and two together, it's him.
The thing is though that Xehanort
never wrote it down anywhere. Either because he didn't care/bother (Sora was not even a blip on Xehanort's radar until DDD when he took interest in him as a third-rate replacement for his 13th Darkness because his two first choices, Riku and Roxas, had become unavailable) or because he simply didn't know.
Even if we do count the brown robed Figure in KH 1 as being the first to see Sora in Person, the event where MX saw Vanitas without Helmet and that event still has a whole decade of time between it. Just like Axel/Lea didn't remember/remark anything on Roxas' resemblance to Ventus (and those two are obviously much more similar to each other than Vanitas and Sora), it can easily be the same for Xehanort.
In fact, there isn't even something really remarkable or important about Vanitas looking like Sora in-universe or for any deep story purposes. It only serves as another visual cue for the audience about the deep connection between Ventus and Sora, as it is only through Ventus that Vanitas gains these appearance traits in the first place.
Vanitas himself isn't even directly connected to Sora in any shape or form.