I use pathogen for organizing my vim plugins. I git clone the plugins from github into the vimbundles directory. This way it is simple to update them.
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I have this line i my .git/config:
[status]
showUntrackedFiles = no
And now every time i run git status untracked files are not displayed. This also speeds up things a bit since git does not check every single file in directory but only those existing in repository.
For more info go to http://git-scm.com/docs/git-config and go to status.showUntrackedFiles.
Edit: Forgot to mention that I also have submodules in bundle directory and I add mentioned option to top-most repository config.