Given that Kryptonians are telepathic (BGDF), Clark could be tuned to Lois on that level - but then the shout from Lois 'Help Superman' could easily be overridden by Lois's subconscious failure to recognize the danger she's in. (Heart rate up, palms sweating? - that's not fear, that's Lois revving up to make the bad guys wish they'd never seen her.)
And if Clark's dealing with a major crisis elsewhere, he may not pick up on a telepathic shout unless it's really 'loud'.
As for SR - he may 'hear' everything, but the speed of sound really is only so fast and he obviously is able to filter things out on a subconscious or semi-conscious level.
My gripe with treatment of the speed of sound (and physics in general) in L&C was in Wall of Sound - Okay, the bad guy has a barrier using sound energy to 'solidify' the air (or some such nonsense). But sounds go through it and so does light. So Clark goes supersonic to break the barrier? HE HAS HEAT VISION!
