As far as I know, it should work in 3.0. As for an autorun file on the NAND causing a probem, you should be able to hold down start+select when you bootup and it will ignore the autorun and allow you to fix it. However, for almost everything, it's much better to use an SD card, rather than using the NAND. Much more space, and you don't have to worry about hurting the NAND (and you can still use autoruns).
If you like the idea of homebrew, for getting the most out of your handheld, I highly highly recommend you go through the GP2X News forum, go through each topic, (using the next topic link) and look at the screenshots and read the brief information about each release. Anything that interests you, download to your computer. When done, unzip them out to your SD card and try them out.
I recently did this, and ended up with around 100 homebrew games which I really enjoy, which I might have never found or explored. There's some really good things hidden away which haven't been updated for a while but are great fun.
Welcome to the community and I hope you enjoy your GP2X as much I have and am