A possible explanation why Andross' brain was a cube was because Andross modified his brain into an artificial intelligence bio-computer which was that cube.

Why is Andross a giant head?

All failed and Fox McCloud himself alone invaded Andross's lair to battle him. When Fox finally encountered Andross, he found that the experiments Andross had conducted had transformed him into a giant, floating head and pair of hands.

Why is Andross a disembodied head?

It is presumed that Andross's experiments conducted upon himself enabled him to become a disembodied entity, allowing the ape to survive in the poisonous atmosphere of Venom and the vacuum of space. Disembodied Head: His massive head is merely a shell of what houses his brain.