Every mod is gonna have its pro/cons, supporters/those who don't.
As for the drawbacks to stacks:
1) If you're looking for a mellow exhaust, and cab-noise is a concern. Don't stack it.
2) You will lose 6-10" of bed space, depending on stack installed and the heat shielding.
3) Have a bed liner sprayed in, the plastic slide-in types will interfere with mounting.
4) Rainwater, though a concern, is easily handled with a small hole drilled at the base of the Y-pipe to 90* connection.
5) Be careful not to go too big / small with the stacks, 5-7" tend to look best and on a dually 8"s
The last thing I would advise, if you tow a trailer particularly, if you're running or plan to run a tuner, and it smokes. That diesel soot will cover your bed and the trailer.
I hope that's a little more helpful, I've been looking at stacks, but they don't fit the rest of my build. Keep us posted with what you decide, and how it turns out.