Even a toughened-up GPS signal may be vulnerable to some future threat. But there are multiple ways to prevent plane, ship, drone, etc. navigation from being completely fooled. Two of these technologies are already built into your smartphone. In addition to GPS, your phone already uses WiFi positioning to locate you when you can't get a GPS signal, and to speed up navigation and make it more accurate. While many ships, planes, and even cars operate far from WiFi signals, there are other signals in the air, for television, radio, etc. that can become part of a non-GPS positioning system to serve as a check-down and navigation backup.
Also on your smartphone is a little device called an accelerometer. On your phone, the accelerometer detects even very slight motion and stores it as data to be used by apps. Advanced accelerometers supported by powerful software have long been used in navigation systems, and they can store enough data to inform the user of location based just on motion data. So an accelerometer system, plus ambient signal location data, could provide excellent backup and emergency location data for any type of vehicle, craft, or weapon system.