No. It's not explicitly stated, but "A rogue cannot select an individual talent more than once."
An Advanced Talent is still a Talent, and the Ninja is still a Rogue.
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More accurately, "Advanced Talent" is a specific Trick, which works like a Rogue Talent in that you can only take a Ninja Trick once (the description specifically states "Unless otherwise noted, a ninja cannot select an individual ninja trick more than once").
So yes, since a ninja has a Trick called "Advanced Talent" and "Advanced Talent" unlike the Trick "Rogue Talent," does not explicitly allow the ninja to take it more than once, a ninja is unable to select more than one Advanced Talent from the rogue's list.