I think it's allowed if it's not of the interest of profit. As long as nobody can use it if they don't have FS9, i don't think it should be a legal issue.
Then again, I might be wrong
EDIT, just read their EULA, and no, you can't edit files and distribute them. As arno said, you can easily just create a polygon in a BGL, so there's no need to edit a default file for the sake of one lake.
Could you not make the lake without modifying the default files? By using excludes and addon BGL files? That way you could distribute it.
Distributing modified MS file is not good indeed. First there are the legal issues as Dick already said. But even if you would be allowed it was not a good idea. Imagine different people modify the same file, that would become a big chaos.
Do not modify and redistribute stock files for any reason. You are breaking copy right. Generally if it is for your own consumption then you can do it although technically it is still not legal. Almost as bad is that modification of stock bgl files can have unexpected consequences including loss of scenery and other elements that you did not want to remove.
However there is a wider point that I can't think of any 'normal' circumstance to do it. You do not need to over write stock files in order to make a modification. All the tools are available to do a 'soft' exclusion of stock elements and then compile your own bgl file that you can distribute and that will have the same effect.