Cost to install shorties or long tubes is going to be exactly the same, with the exception of mid pipes. Obviously if you buy mids (catted or not) or have to have mids made, THAT is gonna cost a little more, but it's the same work to do either.
As for the difference between the shorties and long tubes, the biggest factor is going to be your end goal. How much power do you want and how many mods are you planning?
A used set of 6.4 manifolds/midpipes (plus a reducer for the midpipes to catback) will do most folks just fine. There's a decent gain to be had there too.
As for actual "shorty" headers...long tubes make more power, period. Other than living in California where the inspections/requirements call for carb numbers, I can't see how anyone could justify installing them. Again, it's the same work and almost the same price (depending on where you get them).
I'm a big fan of build once, build right.
If you have the motortrend app, go watch Episode 15 of Engine Masters where they test manifold v shorty v long tubes.