I don't think it's possible for existing Windows code to run in Native Client. As I understand it, NaCl verifies all x86 code to make sure it's safe before executing it, and Wine needs to load x86 code compiled for Windows directly, which will not be using the safe subset of x86 that NaCl requires.
One would need a proper virtual machine to make that work, something like qemu perhaps.
However, the pipelight project may be interested in support for PPAPI.