Having .DS_Store all over the place sucks, but to be fair so does having other dot files, such as .git which is an entire subdir even. At least the convention of hiding dot files from file listings is uniformly observed.
The difference is that .git is only in directories that you explicitly set up as a git repository whereas .DS_Store, Thumbs.db, .desktop and similar get barfed wherever by the file manager without doing anything that a user would consider as a modification to the directory.
