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I think it's heavily implied he had a body. There is nothing else in the series that said he didn't have one, other than that one episode where we saw other members of his race in bubble walkers. Everything else indicates that he had a physical body.
He seemed pretty distraught over the whole thing, which would make more sense if he had a physical body as opposed to a robotic body and the numerous times where he proclaims that his brain is all that he's got left. He was always like that, he probably wouldn't say something like that. He would also mention things like hands and ears. He would say something like "If I had hands, I'd cover my ears, if I had them" That kind of implies he did have hands and ears at one point.
Krang created CLONES of himself and due to the cloning process they began growing bodies. If they were always brain-like aliens, why would they even grow reptilian bodies to begin with. They were all reptiles and I don't think it's a coincidence because Krang would croak numerous times, kind of like a lizard or other reptiles. Even Beserko didn't really recognize him until he overheard Donatello calling him Krang and remarked that he had a body the last time they met.
I think it's much more likely that he had a body. When you add it all up and put two and two together, it begins to make more sense.
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