I did my mounts recently and didn't disconnect any wires. The ABS wire on the passenger side was the only wire I could see that might cause an issue, but it was just long enough to get the job done.
I can confirm that leaving the dog bones connected can cause popping noises. I left the opposite side on to help keep the engine from sliding out of alignment. Worked fine for the trans side, but I had to take it off for the engine mount simply because it was just barely too low to pull the mount out. Ended up prying the crap out of it to get that side to line back up, but the trans side just dropped right in.
