Jimmy,
I've heard for years now about warped valves from short exhaust systems, but so far no one has been able to produce a set of them... I suppose it may be possible from running the exhaust straight out of the exhaust ports themselves, but I still somehow have my doubts.. Back in the sixties, many stock cars on the local short tracks ran what was called "stubbies" headers. Basically short lengths of tubing maybe only a few inches long at the most in order to keep the plug wires from burning.. Heck, they burned anyway, but mostly because we had not yet invented silicone jacketed wires! LOL. My point is that many of these cars ran this way week after week for an entire season or more with no apparent ill effects unless you could blame a thrown rod or blown piston on the exhaust..
The megaphones can serve a purpose in regard to building more horsepower or altering the torque curve. However, there is a lot of science that needs to be applied given a large number of variables. I know (knew) of only two people that ever really addressed this in real life and actually made it work for them. One of them was Smokey Yunick, the other was Ed from Headers by Ed. Both men looked at the balanced package holistically in order to design the exhaust system for the particular needs.
I could write volumes about this but unfortunatley do not have the time. I had talked with both men for many hours about this subject (and others of course), but both were adament that there was no such thing as a one size fits all approach to exhaust.
For our purposes here, the megaphone will serve only two purposes:
1) to look good
2) to make a LOT more sound
As far as the sound is concerned, it is typically a deeper and much louder as the pressure waves are expanding and being focused.
Jac Mac and others I am sure can chime in here with more information.