Clive has just answered the home/limit question - Mach3 knows what you are doing so treats the switch inputs accordingly. There is a minor gotcha with this. If you use a switch with effectively no offset between on and off positions, you can get problems (to be more accurate, I had problems) with this. Z homed, then X and Y started moving. The Z switch had swapped from homing to limit function, and the slight vibration caused the Z switch to trip and stop the machine ("limit switch event"). Fortunately, the IP/M has the capability to move the axis very slightly away from the home position immediately after homing which fixed the problem.

The limit on number of inputs only applies if you are using a parallel port. That statement on the Mach3 config page is a bit misleading. There are only five input pins on a parallel port as all the others are output only, so the limit is a physical one and nothing to do with Mach3. You will be fine with the IP/A and are free to use all the ports. I doubled up my switches (combined upper and lower) mainly to reduce the number of wires needed and I still have some unused inputs on the IP/M.

Don't worry about voltages. Desertboy was talking about Arduinos and they are definitely 5V only. The IP/A will be very happy with 24V signalling, and in fact this gives much better noise rejection. The CSMIO kit is built to use the industry standard 24V signalling. No pull-up/pull-down resistors needed, but watch the wiring instuctions carefully so that you get it right. Less flexible motion controllers only have one input pin but there are two per channel on the IP/A. There are plenty of examples of how to wire NPN n/c proximity switches in series if you do a Google search - I have had four in series working reliably in testing although in practice I only wire them in pairs on my machine.