According to Rick, the Rick's are so clever that they have their own brain waves. The bad Morty is clever too, so then why did the Rick's did not notice him?
Evil Morty is generally surrounded by other Morties. Even if he does generate Rick-like brainwaves, they would be masked by the other Morties around him.
Additionally there is no reason to think that brain wave scanning can be done automatically and Ricks are dismissive of Morties. They might have never thought to scan him.