Yes someone has been cheating with changing values from memory or changed the rules in the XML files.Both very easy to do.
Yes, people have been editing files to make monsters give more XP/Points. A anti-cheat for the leaderboards is being worked out the last I heard, so don't worry about it.
We'll reset the highscores at some point soon, with a balance patch I imagine, and look into making it a touch less convenient to cheese the numbers.
The problem is that unless you have a side-program to check for the game's memory while its running for changes made by 3rd party programs your leaderboard won't be able to know if this guy cheated or not. Blizzard Entertainment uses a hidden application named "Warden" that monitors their games' memory but making such a program efficient could be hard work and may also cause privacy concerns from users.
Yeah, clearly it's impossible to completely stop, but at least it'll stop the dumb people that find the highscores file.
The same guy has 1 billion on another difficulty. It really is impossible to stop this kind of thing from happening though...
ArchoX: Open up Steam, go to Community, Search for Dungeons of Dredmor, click on View Stats, then click on Global Leaderboards. From there you can choose difficulty also.
@afterstar There's also the stdout file that could be used to help with this. After a bit of meddling, the stdout file says that I've gotten 9001 exp from killing a single diggle. Quick, easy to notice problem.