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This past week was my first at Lullabot, so I'm still learning how they typically do things there, but I've always included the full Drupal core and any contrib modules in the repo.

I've avoided git submodules because support is still iffy on some hosts, if you're deploying from the repo hosting service. IN particular, Beanstalk only supports the master branch of any submodules, and that's what we used at my last employer.

I'm sure there's a better way to handle it, but I haven't found it yet. However, I also haven't looked very hard, because I haven't had enough client sites to maintain at one time to make it worth spending the time to dig into it.