Many of those systems were designed before GPS became operational, but even now relying on GPS is not particularly prudent.
(There's also 'GPS jamming', which is totally a thing in war, but that's not really 'like our phones', generally.)
As other posts have mentioned, though, GPS is simply one input into weapons systems, not the input into weapons systems.
Civilian grade GPS receivers are intentionally crippled to stop working above some altitude/speed limits.
EDIT: It seems that the COCOM limits apply only after "1,900 km/h at an altitude higher than 18,000 m".
However, looking at the ublox receivers as an example, they have to be explicitly configured to operate at aircraft-level speeds, which smartphones likely aren't.
The LGA to DCA one had a max speed of 461mph (average 322) and altitude of 23,400 foot, with maximum negative gradient of 67.7%.
Maximum speed I've recorded overall (I've had the app open for 24,190 miles) is 673.3mph, and max altitude of 35,081 ft
It's encrypted, so it's not for civilian use, and the ability to look at two signals of different frequency at the same time means that they have been able to have much more robust GPS than civilians for awhile.