James,
The home switches are a Hall sensor that is normally closed, so when it triggers the circuit drops low. The Y limit switch has more LED's because it also has the indicator for the A axis Hall sensor and the power indicator LED right next to it. You are correct about the magnet. There is a fixed magnet that is mounted in the main block. You can see it if you jog the X axis forward and look at the back of the main block about a half inch to the left of the X motor.
When you jog the X axis across its home position at that back of its travel, (across the magnet) can you see whether or not the indicator LED stays on or does it flash when it crosses the home position?
Jonathan