Ah. People after my own heart. I also like to use the right type of gun for each game. I currently have 27 gun controllers with a range of fixed (positional guns) IR guns and real light guns. It makes the experience more arcade-like.
From memory, it states that you can use up to four aimtraks on one machine so it should be possible to put two aimtrak modules in happ arcade shotgun shells and leave two as pistols. If they really like shooting games though, I would advise them to put a PS2 in the cab instead (or as well as). The PS2 is unrivaled in this genre. No other platform even comes close in terms of the quality of titles and availability of low cost high quality light guns. The official Namco Guncon 2 is head and shoulders above any other home light gun.
If it has to be Aimtraks and they are using a flatscreen, it is worth noting that the Amtrak software allows you to set each gun up as either a mouse or analog joystick. If you have problems related to setting all four up as a mouse, you could try switching two of them to work as analog sticks. This is better for fixed gun games (like T2) anyway.
Do you know which gun shells you'll use yet?