As of right now, there are three different fully operational worldwide satellite navigation systems -- GPS, Glosnass, and Beidou. Plus there are three others (Europe's not-quite-in-service) Galileo, and partial coverage systems fielded by Japan and India. So if some hypothetical adversary "took out" GPS, there would still be several other systems from which positional information could be obtained.
I have no explicit knowledge of this, but it also seems to me that warships might have inertial navigation systems as backup to GPS. US submarines stay underwater (and therefore out of GPS's reach) for long periods of time and it's claimed that their INS's are amazingly accurate.
If GPS is taken out in wartime, the best bet is the other will be too.
Alternatively all the systems could be disabled by a direct hit from a Coronal Mass Ejection (CME).
I assume that the USN is also implimenting procedures for maintaining good time, i.e. multiple clocks and recording error rates.
As far as intertial goes, the accuracy of the position degrades over time. For a boomer sub if the error adds up to 5nm or more after 2,3,4 weeks, that's OK operationally, position is corrected when they come shallow to fire the missiles. For other subs they are coming shallow more often.