Back with legal opinion of learned counsel, a professor of international law:
1. The "complete and exclusive sovereignty" a state possesses over its aerial territory ends at the uppermost height at which aircraft are capable of flying. Altitude of 90,000 ft is unique to this single aircraft and so it must be excluded from the general aircraft class.
2. The Bogota declaration of 1976 never applied to Cuba, which was not a signatory.
3. The Latin legal principle "Caveat humana dominandi, quod omnes tangit ab omnes approbatur" (what concerns all must be approved by all) doesn't apply as there is no international treaty, so by analogy the Law of the Seas relevant clause asserting the existence of "
a zone of innocent passage"applies especially since Cuba never alleged its citizens were endangered by SR-71 overflights, so the Law of the Seas treaty applies.
Anyone wants to argue legalese please apply elsewhere - I only represent that I faithfully reproduced here what the professor actually said