A few related things that catch people once the project has moved.
Access Linux files from Windows through the network path that the subsystem exposes, not by hunting for the virtual disk file. Explorer and Windows applications can read and write there. It is slower than native Windows access, which is the mirror image of your original problem, so use it for occasional access rather than for a build.
Do not edit Linux files with a Windows tool that rewrites line endings unless you have configured it. This produces a class of confusing failures where a script suddenly will not run.
Backups. People move their work into the Linux filesystem and their backup tool is only watching the Windows drive. Worth checking before you have a month of work in there.
Disk space. The virtual disk grows and does not automatically return space when you delete files, so it can consume a lot over time. There is a compaction procedure; worth knowing it exists before the drive fills.
And on your original symptom, for anyone reading later with a smaller version of it: if something is slow only when it touches many files, and only in the subsystem, it is nearly always this and the answer is nearly always to move the files.