Not necessarily. If he truly believed that there were still Andalites on Earth, they wouldn't figure it out. Let's face it, Visser Three has an Andalite host, and he never figured it out.
They must have seen the dome go down, but Elfangor still got past their defenses, same with Gafinilan(sp?) and Mertil.
Plus, it would definitely be an odd twist. The second Andalite Controller. Do you think Visser Three would take the younger Andalite for himself?
And I still think he'd end up joining them without really thinking about what he was doing.