What kinds of modifications are you talking about exactly? I've seen no 3G-related hacks for the Kindle.
The only problem I could see is if the FreeDownload hack was made to work with a 3G connection instead of only Wi-Fi. That'd probably get Kindles using it banned from 3G, as it'd allow a lot of bandwidth to be used up (as opposed to the allowed .prc, .txt, .mobi, and .azw formats, which are usually books and small file size).
I have the jailbreak, screensaver hack, and freedownload installed on my Kindle 3G and there's been no problems. Of course, it's not as though I've gone and told Amazon I put these on there, but I don't think they run scans for them or anything anyway.
Besides, didn't somebody here say that Amazon said they did not support these hacks, but they won't void your warranty? Don't quote me on that, I'm not sure if that's true, but I will email Amazon soon asking about it.