Obviously the main difference between shorties and long tubes is the length of the individual exhaust runners. But what's been left out of the conversation is the effect of the different lengths have on the scavenging of the exhaust. Long tube are designed to time and blend the exhaust pulses at high RPM with the least amount of piling up if possible. But even so, they are not exactly a one-size-fits-all but more of a ballpark guess because they have to be designed for what the builder considers "average" cubic inch, cam, +/- supercharger, etc. Somewhere in all the possible factors will be a combo that is 100% optimum for the headers and everything else will be close but not 100%. This is not a put down on the long tube headers because they are the best thing since sliced bread for high output, high RPM conditions.
But it's not all doom and gloom for shorty headers because while they do give away some of the high RPM advantages, they are still a lot better than the stock cast iron, boat anchor, manifolds. And they bring possible benefits that long tubes don't such as excellent response from off idle up to nearly maxed out RPM in the cars that are driven on the street 95% of the time. Everything is a trade off and shorties have their place and might be a better choice for more folks than you think.