Only 1 JVS device can be plugged directly into the NAOMI unit. Each pin of the two ports are wired together, I believe they used a double stacked port just to help with clearances against the case. If your NAOMI still has the original unmodified case then the inner port should be completely obstructed.
JVS protocol supports many devices though, they just need to be chained together, so the first device plugs directly into the NAOMI and the secon device plugs into the first device, and the 3rd device plugs into the second device etc.
This is how JVS VS play works. Cab 1 has the NAOMI and the JVS Device 1 for P1 controls, Cab 2 has JVS Device 2 for P2 controls.
I've also seen some 4 player games use similar setup with JVS Device 1 for P1 and P2 and JVS Device 2 for P3 and P4.
Similarly the Trackball games have a separate JVS device that is the second in the chain for the trackball while the all of the other controls are on JVS Device 1.
There are other chained configurations as well.
