Yes, they're in KIAS. No, FMC holding speeds do not increase with altitude. That's the gist of the problem. They researched acceptable speeds and apparently realized the Vref +80 (+100 > FL250) was always an acceptable holding speed.

For those flying 737NGs with winglets--how much of a difference do they make in glide performance?

Based on some generic numbers, you can make an estimate. Lets confine our thoughts to low altitude (ie less compressibility), and a rough figure of 6 % better specific range at max range speed (you should be able to get an exact figure from the performance sections for the aircraft with and without winglets). Assume a flat thrust curve vs velocity.
You've now got approx 6 % less total drag, even though the winglets add parasite drag, and the added weight gives added induced drag. However that is at max range speed about 1.3 times min drag speed. So at min drag speed, expect about 5% less drag (induced drag will be higher at the slower speed, but the reduction of parasite drag will be even more since it increases with TAS squared).
So, expect a 5 % increase in glide distance. It it was 20:1, expect about 21:1