the input delays on the APM are virtually negligible. Using the handbox has an unusual characteristic of always seeming to lag your inputs by a 1/2 second or more.
For the second question, I don't know but I think not. The APM seems to override the normal drive commands (like what the PEC inputs are for instance) but I would guess that the serial input for the handbox might get hangups about two apps trying to drive it simultaneously. I've only tried hooking the handbox to the serial port on the computer, and parallel port guide software to the APM from the same computer - not trying two apps through one port.
edit - this just in from (http://www.users.on.net/~pbl/art_autoguiding.htm
The parallel port and relay interface method is considerably better for guiding. Dick Seymour has reported that the serial method updates the scope position every second or so but only if [autostar handbox] resources aren't being directed elsewhere at the time, whereas the APM autoguider method updates the star position 10 or more times per second and is independent of what the scope may be thinking at the time.