Ok, here's the deal.
1. Yes, a tune can cause a loss of torque. If the timing, air, and fuel are not set up in the ideal situations, then it will cost some torque.
2. Long tubes can also cause a loss of low end torque if they are over sized for your application. For example, if I were to run 2 1/4" primaries on my 460 build, I would not have as much low end grunt as I would if I were to run 2" or 2 1/8" primaries.
3. No, you should not. What you should do is go somewhere where they actually create the tune while you are on the dyno. The "canned" tunes you get from dealers like Kenne Bell, Procharger, etc, are a "one size fits all" type of tune. There are a lot of variables like elevation, temperature, humidity levels, etc that can affect a tune. So, these canned tunes tend to be on the conservative side for safety reasons. A custom tune is written for your car, at your location, for your weather conditions. It is the best way to get the most out of your car.
It doesn't matter if you go with Sniper, SCT, Diablo, or any other tuning software out there. They all do the same thing...tuning is tuning. All they do is change the parameters in your computer for the different load levels so your computer knows what to do. All you need to do is find someone that actually does custom tuning with the sniper instead of someone that downloads a tune from sniper and loads it into your car.
"When I know more, I'll be forthcoming. Or I won't be forthcoming, and I'll be honestly deceptive." - Les Miles