Please tell me if there's a way to make git-grep (or git-log for that matter) work between submodules.

While I may not personally like behemoth repositories, I do see why people would choose to endure them. They do have their advantages, even if they all eventually end up looking something like BSD ports. (FYI: I happen to like the extremely modular one-git-repo-per-component approach as used in Mer. Hell, I did an early implementation of the OBS+git -based autobuild system back in 2009!)

Sometimes the cure is worse than the disease.

git submodules don't fix anything except maybe a good day.