Doesn't "一体!?" fall among the lines of "What is it exactly!?" here? Wouldn't he have said "一隻!?" if it had been about single unit?

Depending on what he see the object as. If he see them as human(-like creature) or monster, he could use ~体 as counter.

Well, I thought it was "single unit" because the fairy alert him about the enemy then right after that, he made an assumption that it was the enemy Flagship.

If it was "What is it exactly", the dialogue wouldn't be that logical I think.