They are on separate traces as far as I can tell (if I remember right). I traced everything out a while back looking for a hardware solution and I'm pretty sure I traced the analog stick datalines back to the CPU.
All the actual hardware buttons are wired to this chip:
Unfortunately, there are no identifier markings on the chip in either of my 18A's so no way to look up a datasheet or similar. I marked pin1 in the pic above. here's what I got when I traced things out.
The following pins connect together when the buttons are pressed to register a "button push" on the chip:
Right Trigger = 12+15
Left Trigger = 3+15
D Pad Up = 2+10
D Pad Down = 1+10
D Pad Left = 2+9
D Pad Right = 1+9
OK = 4+14
A = 4+15
B = 12+14
X = 3+14
Start = 11+14
Select = traces go to the CPU
Function Button = 11+15
Esc = traces go to the CPU
Its possible to rewire things differently and still replicate the same button presses through different pin combinations. Its too confusing without a datasheet to figure out though, so I gave up.
EDIT: Also, why in the name of god they did things this way I'm still trying to figure out. I think it would have been a much better design decision to just integrate some kind of built in USB interface type gamepad with drivers for it built in.
I'm actually waiting for an ICS rom that doesn't suck so that I can just cut up a usb gamepad and toss it in the case and rewire the buttons to it. Should take care of things pretty much. i'll probably even score some L2/R2 buttons out of the deal.