I'm color blind and I reviewed "BioShock 2." You'll note in the review that I didn't mention having issues with the hacking system, and that's because I didn't. There have been games over the years that, because of palate choices, were nearly impossible to play (the "Puzzle Fighter" series is probably the most glaring), but "BioShock 2," with its color-oriented hacking system, was no problem at all.
Negative Gamer put together a nifty feature which tries to recreate what color blind gamers see when they play "BioShock 2." If you're curious, I guess I would fall under the "deuteranopia" category, which is the most common form of red-green color blindness.
But, in the case of "BioShock 2," I had no problems distinguishing the reds from the greens from the blues in the hacking minigame, so clearly some effort was put forth by 2K to ensure that certain color blind gamers are considered. Also, in Negative Gamer's piece, it would appear the only color blind condition that would make the game nearly unplayable is tritanopia, which is super uncommon. I'm not saying those gamers with tritanopia should be ignored, but sometimes in game development you sort of need to play triage with accessibility.
There is, however, a catch-all to ensure that color blind gamers have no problem with your game, and that's including supplementary patterns on top of the colors. For example, the "Puzzle Quest" series does this quite well, as do most of the PopCap games, like "Peggle" and "Bejeweled."