Longtubes give an advantage in the low-mid range.
However, where most people race (3,500+) the shorties are right there with longtubes. Some have even seen 'peak' gains with shorties above a longtube combination. Now peak doesn't mean much
Generally speaking, there is not a big difference at the track, over longtubes vs. shorties.
I took out my old 172,000 mile engine with a new 306, ported my performer lower professionally by tmoss, and added longtubes over my dented shorty primaries and partly crushed old H-pipe, and gained 1.3 mph, the equivalent of 13 hp.
Take that for what you will...
If starting from scratch, and you got the extra dough, go with longtubes, unless you have emission standards to keep up with.