As you may know, most proxies don't cache resources containing a query string. Is it the case for Polipo?
I had a look at the sources of Polipo.
As far as I can see, there are no verifications done at all on the URL to be cached. The only part of the URL that it tests (in routine httpServerRequest), is the port number for implementing its option of allowedPorts.
My conclusion is then that Polipo does at the moment cache URLs with query strings. But of course this can change in future versions.