I stand corrected - it seems it was electrodes rather than implants. Some interesting comments on the old Slashdot story:
http://it.slashdot.org/story/02/03/14/2051228/airport-securi...
From reading the New York Times article, it doesn't sound like Mann had any "implants" "forcibly removed". It sounds like they tore electrodes off his body. In other words, they pulled tape off his skin, and it caused bleeding. Unpleasant, sure, but it's not like they strapped him down and used a drill to extract chips from his brain. More like they pulled off a Band-Aid too fast.
The reason that he ended up in a wheelchair was that since he no longer had his cyborg navigation gear, he supposedly got confused while walking around the airport and hit his head on a pile of fire extinguishers. I don't even know where to start with that one.
And another comment, which may explain the doctor's note:
Years and years ago, when the earth was new, I was an undergrad at MIT and then-Media-Lab-graduate-student Mann spoke in a class I was taking. At the time, I believe he was trying to recruit people to do heavy-duty graphics work (i.e. when he moves his head side to side, his camera is taking discrete pictures of a room/building/whatever at different angles. He was working on algorithms to put them all together and make them coherent). Anyhow, the point is, I distinctly remember him saying that he got nauseous when he removed his visor. The reason was very simple. He spent all of his waking life (outside of the shower) in a 2D world. His body was so used to it, that living in 3D took some serious getting used to, and he would feel sick. My guess is that this is what happened. Ever feel like your eyes need some adjusting after staring at a 2D object (such as a movie theatre screen) for hours at a time? Now image doing that 24/7 for years and trying to re-adjust to the real world.