Amiga towers tends to have 3 LEDs, and red is normally used for hdd activity, yellow for diskdrive activity and green for power on.
Even though some towers have connectors like you descripe it doesn't go anywhere on the Amiga motherboard. I think it's because some towers are aiming at using a specifik keyboard adaptor.
I have a RBM tower for my A1200, and it has the same connectors, so I had to hack all 3 LEDs in order to get them working/connected. I later found out that there where a specifik keyboard adaptor for my tower, which has the prober connectors for the LEDs...
