According to the Hork-Bajir Chronicles, the future Visser 3 is the Yeerks' greatest expert on Andalites, and would become an ever greter expert when he took control of Alloran.
When the "Andalite Bandit" attacks began, I expect that Visser 3 would use his vast Andalite knowledge to predict Andalite bandit attacks, unaware that they were mostly human. As time went by, Visser 3 should notice that the patterns of the "Andalite bandit" attacks don't fit the Andalite profile. This should cause Visser 3 to wonder if he is really dealing with Andalites.