This has been talked about before, a couple times... Couple things to point out here...
For one, none of the Custom Dice places will do Shadowrun dice using the SR Logo (Or any other trademarked game logo). At least, they shouldn't, and I know Chessex won't. They don't have a license to produce dice using those logo's, and doing so could get them in trouble with the game companies.
I've heard CGL folks mention interest in doing SR Dice. Drop them a line and let them know you're interested. We're starting to see some extra merchandising creep out now beyond the books, since CGL has a full on license to play, so they had Patches at GC this year. With the 20th anniversary next year, I'll be very disappointed if we don't see something like this pop up. (I also want SR logo stickers and window clings, and T-Shirts in Ork and Troll sizes.
).
Beyond that, yeah, the above suggestions for painting/coloring dice work pretty well.
For my own use, I have a set of
custom dice with my Ork Smiley logo that I had made by Chessex last year at GC. They're not really SR specific, since the Smiley just appears on the "6", but whatever. I can pick out 5's, 6's, and 1's easy enough that color coding wouldn't really help me any. But SR dice would be fragging cool