Are you sure you're actually disabling the app and not simply removing the shortcut? Once an app is removed or disabled it wouldn't update from Google Play.
A way to check,
- Open Android Settings
- Go to Apps
- With the filter set to "All apps" scroll to the app you want to check (i.e., Google Maps)
- See if there is "Disabled" text to the right of the app, if not tap the app's icon
- In the App info screen, select "Disable", if you're promoted to uninstall updates press Yes