why the future “estará” here instead of “esté”?
In short, because you’re describing something real (i.e. not knowing something), not an opinion, or an emotion or a hypothetical.
makes sense, but why the future tense instead of present?
That’s a way of expressing conjecture or supposition.
By the way, this is an indirect question; compare with “¿Qué estará pensando?”. Using the subjunctive would just not make sense.