Thanks for the replies. First off, no automatic here, only stick, so the tranny wasn't a concern for me, although I imagine it isn't the best on them.
I've watched some of the big dogs in Stock and SS and most seem to shut the engine off or at least go to neutral, then restart for the drive back to the pits. Again, talking about stick cars mainly. My concern, as David mentioned, was for the rods. Mainly because I imagined the extremely high vacuum under deceleration had to stress them out, even if they're steel. I could also see it causing some ring flutter, although i haven't heard of that before, as well as trying to suck the valves open if seat pressure wasn't sufficient. I don't notice my car porpoising, although I have seen that on rigid rails and big tire cars as mentioned.
I think I'll start using brakes only because I just can't see it being any good on the engine. I need to get my rotors turned because under hard braking from 100+ mph I can feel they're slightly warped. Thanks again for the replies.