One system used was and is an enhanced astral (astro [sic.]) tracker very similiar to that installed in the B-52's before inertial and GPS. Very, very, very simply put it locks onto a star or celestial pattern and tracks by angular offset which is summed with time and altitude and a few other things.
The system is needed for the SR-71 because the speed and altitude at which it operates can put it outside of the parameters needed to keep four or more satelites in "view" for GPS and DME slant range becomes essentially irrelevant.
Clouds have a highly adverse effect on its accuracy so the airlines wouldn't be interested even if it were available.