Yup, I've run into some games where WASD and the like are scattered on Dvorak. What's worse is occasionally it's inconsistent, and they use key codes for some things and letters for others. I've even had cases where they somehow read the primary keyboard and I had to reorder my keyboards in the settings for the game to work properly.

Bigger budget, newer games are usually more consistent, but all bets are off with older games.