Would fully binary communication even count as a language, or would it be more like direct communication of computer brainwaves, more like telepathy?

Words are effectively communication of human brainwaves, so it would probably be considered a language, yes, since it lets two machines effectively talk to each other.

Do stenography chords count as a language of their own then? SKRET T*EBGS is hardly intelligible as a way of constructing letters normally.