Choosing a turbo between the ATS and BANKS systems is pretty much the same just what options you want it to come with (like gauges and exhaust).
As you mentioned you said you are not going to be worried about the exhaust so that pretty much says to me skip the Banks unit. Now you need to look at how you want the turbo located on the engine.
Banks is centered over the intake manifold at the rear where as the ATS is off center a little towards the passengers side. I hear from the guys that have the ATS that getting to the glow plugs on that side can be a pain, I know that when I had The Enterprise that I could get to all the glow plugs pretty easy except for where the glow plug relay was relocated to but seeing as how you have a 6.9 that would not/should not be a concern. once you bring the ATS system up to the same level as the BANKS the price is the same but your not going to be interested in the exhaust because your going to do your own. So I would recommend the ATS if you want a wastegated system or Hypermax if you want a non wastegated system.
Now talking about WG vs NON WG. Biggest thing you will notice between them is that the WG turbo will pull from the instant you mash the pedal, the NON WG turbo will lag some (in my opinion it's actually quite noticeable) I wanted the power right off the line at very low rpms so WG was the way for me. I have driven a NON WG Banks (early version) on a comparable truck and noticed the lack of off the line power right away, but at speeds it pretty much felt the same.
Hypermax does not come with an exhaust system that I'm aware of it's cost is lower than either ATS or BANKS.
Now here is the differences that I seen when shopping between the ATS and BANKS
Banks comes with these extras that ATS does not
Gauges - pyro and boost
exhaust (on top of that banks comes with 3.5inch vs the 3 inch that ATS sells as an option - ATS assumes you will use the stock exhaust or fab up your own).
Transcommand (only for the 7.3's that are equipped with an E4OD) - this will not be a concern for you.
I ran my system with and without the muffler. Performance was about the same, did shave about 50 degrees off the peak EGT's when making a hard pull, but overall I did not see much improvement. I will say that after I lost the muffler she sounded better but while making a long pull up a grade with the TT strapped to the back it would sort of drone on you after about 2 hours of screaming down the highway. I looked at adding it back in more than once after taking a trip because of that reason. But around town she sounded pretty good - had a nice rap to the exhaust note at around 2100rpms - sort of like a gasser big block.