I personally don't use EMC, but I think it would be the same in principle as mine.
I have a similar situation with the number of switches except I only have one switch on the X axis that will trip in EITHER direction (so you might say it is two switches in you case). My switches are wire NC (normally closed) and in series for the axis's with multiple switches. You want the limit circuit to be NC for safety reasons. The main one being that if you have a wire failure, the machine will stop as it will detect a limit trip. If you wire NO (Normal Open), you will not know about a wire failure until you crash something!
Ok, that takes care of the Limit switch problem. Now for using them as home switches. You only have to be careful in this situation that an axis switch is NOT tripped in the wrong position. To explain, if you normally home to the X - position and if the X + switch is tripped, the table will move in the wrong direction! Otherwise, things operate normally. So far in my setup, I have not had this situation occur.
To answer your question on if two axis trip at the same time, the controller doesn't care and usually a visual check of the spindle location will tell which axis is tripped. The only time I have had a problem with this is on occasion I would get a "false" trip for some unknown reason. I think this may be due to noise on the system or a possible "feature" in my control program.
Hope this helps.