Some insight here...
The SE usually had a red LED when it shipped with the 20MB MiniScribe. I have seen the odd MiniScribe with the amber, but almost all seem to be red.
Amber lights became more common in 1989 when the SE shipped with other drive capacities inside. The 40MB drive seemed to get an amber LED.
Every SE/30 I have seen has an amber LED, regardless of capacity, though I don't doubt the greens because...
...I have seen the green on a factory SE. It was a SuperDrive model and I believe it was manufactured sometime in early 1991. There could well be some SE/30s with that as well. I do remember that particular SE had a 40MB drive.
For what it's worth, the Iici I have came standard with an 80MB drive with an amber LED for its hard drive (and a green for its power light). It's a mid-1991. I think amber was the most common LED by then, with red almost phased out entirely if not entirely, and green sometimes getting mixed in (though rarely).
Also, check the access lights on the ZFP SCSI drives (20SC, etc) back then. I've seen all three colors on them, although the only stock green I've encountered is on the HD20.
Last but not least, don't forget you can retrofit them. Does anyone know the exact size of the cable needed? I had to do a little soldering work to get an LED wired up once...put a blue in an SE just for fun.