Which maOS version are you using?
As I understand it, it's the websites and the search engine that determine which map will open.
When I search for 1 Apple Way, Cupertino CA in Safari with Duck Duck Go as the search engine, it goes to an Apple Maps link. When I search the same address using Google search, it goes to a Google Maps link.
Are you by any chance hitting command-click that would open the link in a separate tab?
When you say it goes to the App Store, does this happen only for a Google maps link?