I'm not sure this would work - if an operation needs you to stat() a file for every file in the repo (for example), whether it is 10k files in 1 repo or 1k files each in 10 repos will probably just as bad?
Any time you were pulling the entire repo tree, it could be slow, yes. But assuming people are only working in one or a small number of repos at once, you can imagine a workflow that didn't involve nearly so many operations on the entire tree.
(I almost habitually run "git status" whenever I've task switched away from code for even a few seconds to make sure I know exactly what I've done, which would have to look over the whole super-repo as well.)
Thankfully we're a while away from the times based on the synthetic test - it's not something I notice at all, but I probably write less code than most engineers here.