Frome experience git is slow on windows when dealing with 10's of thousands of files even with a SSD drive. This is due to the filesystem (NTFS) being rather slow, especially for various stat operations. (If you watch in windows taskmanager this shows up in the "other i/o" column -- not reads or writes.
I don't know why, but NTFS metadata performance just was never very good. I always assumed that was due to the more complex/capable data model compared to what Linux usually uses, but I'm not so sure about that any more given the complexity and yet still better performance of ZFS (btrfs remains too much of a mixed bag to mention here).
However, poor or bad applications also play a role here. For some reason explorer.exe requires 1-2 orders of magnitude more I/O time than dir.exe, and somehow the local search is slower than a human binary search. However they managed to do that bad of a job remains a mystery.
Yeah, poor search performance is definitely an application problem here. Lately I've taken to using Cygwin find instead and it runs just as fast as you'd expect. eg
