My entire lab is filled with EE's focusing in neuroscience and brain-machine interfaces. We use implantable electrodes though, much better SNR and fewer corrupting noise sources.
Usually humans. I'm not involved in this kind of research, but BCI with implanted electrodes probably refers to cases where these electrodes are implanted for some other reason.
For example it can be necessary to find an epileptic seizure hot spot because you can't stick someone in an MRI tube for a few days on end.
It's hard to actually make a case for BCI as an assistive technology, because every single sceletal muscle in your body provides a better input signal than EEG ever could, and there aren't so many cases where people don't have any voluntary muscle function left. (My opinion... need not be correct!)