As far as I can tell, Samba has no way of using a certain WINS server for a specific interface

I think the idea is that if you need that feature, you just run two instances of Samba, one bound to each interface. This, I believe, is a limitation of how it binds to the interfaces under Unix. It doesn't bind to each interface explicitly, but to 0.0.0.0, which just gets everything, and once they've done that, there's not any way to distinguish over which interface packets came from.

But I could be wrong.