https://github.com/pnpm/cmd-shim/blob/master/index.js#L464
This is a question first, but the answer might point to a bug in normalizePathEnvVar
On Windows, it looks like each path in NODE_PATH is prefixed with /mnt/. I'm unfamiliar with Cygwin, but I use WSL a lot. WSL initially mounted Windows drives as /mnt/c/ but these days the /mnt/ prefix is usually omitted, so it's mounted at /c. Might that cause problems with cmd-shim?
I don't know how NODE_PATH is being used, so I'm not sure.