I don't have a IIci so can't do some of the leg work on this, but the Guide to the Macintosh Family Hardware documents bit 0 of register A of VIA1 as "reserved". This bit is pin 2 of VIA1, and should connect to the diagnostic edge connector with a pull-up.
The II, IIx, and SE/30 are documented to have 3 bits (0-2) of that register as "reserved" as well, also going to the edge connector. I've got a small control panel that toggles that bit and controls an LED on the IIx.
So, if you can find the VIA1 and get to pin 2 whether it's the edge connector or the pin or whatever, that can be used to control the LED from software.