If a Super guy could chime in and tell me I'm wrong I won't argue, but I recall being told that the cant angle on the stores actually is better for aerodynamics even at speed because of the way the bow wave and area rule are in effect on the jet.
First, I am not a jet guy, and I make no claim to be.
That said, I spoke with "Knockers" Niewoehner last summer about this and he said it is pure fiction. The cant was put because of fears of poor store separation (the CFD simulations looked bad AND they had at least one hit the fuselage in early dev test). In op test, it was found that the cant was really unnecessary, but by that point, the line was already up and running and re-tooling would have cost a fortune and delayed IOC. He didn't have an answer for why it's never been changed, though; he suspects $$.
FWIW, he said the guys doing the RCS work on it hated the canted stores, too, so it ain't an LO concern, either.