Running user-representing software on your phone doesn't fix all problems everywhere, it just gives you a platform with which you can address them to the fullest extent possible.
I would think they are certainly using phones to collect Wifi AP locations. In fact if they've stopped doing so with the mapping cars, then it's probably because the phone backhaul is good enough.
The ways of preventing this are much less straightforward though. Stopping your phone collecting them will only remove some datapoints (perhaps significant for some people, but not for most). Disabling AP beacons or continually rotating ssid/bssid can mitigate it for your own APs, but at the cost of some UX.