on the V6 GT, there are 4 cats: 2 'precats' in the manifolds, and 2 'main' cats underneath the car. each is associated with a lambda sensor.
i believe that removing the manifold cats does not trigger the CEL (check engine light) as long as the lambas are refitted properly. so you could use non-cat GTV or 164 24V manifolds, or aftermarket like Supersprint or Unicorse.
this is what the factory manifolds look like (these are actually off a 147GTA) vs GTV non-cat versions that have been sprayed and wrapped (photos courtesy of ALFA_001):
changing the manifolds should apparently bring some of the biggest benefits, BUT is also the most labour-intensive. removing the manifolds is major work from what i hear; official workshop manual suggests removing the engine, but it can be done without this, but still requires much of the surrounding piping (cooling, aircon) to be dismantled.
thus far, i have kept the original manifolds. i am not chasing maximal power, so i'm reluctant to go so far. but i have changed the main cats, to 200-cell high flow versions like mentioned. these are built in Australia by HiTech Mufflers, Sydney, who are somewhat local to me. saved 2.5kg in weight too.
by law, my car must have these cats. i should be able to get away with new manifolds though, in the future if i so decide. if you remove these main cats, you are VERY likely to trigger the CEL. does this result in the engine going into 'limp home mode' (major cut in power)? not sure. but there are adaptors you can screw into the ends of the sensors to trick them into think everything is 'normal'; Glenwood sell them i think, from reading around here.
my new cats have added a very small amount of power to the car. around 4kW at the wheels on pre and post dyno runs. now, following more 'time on the road' and an ECU reset, i think it would be a bigger improvement if i put it on the dyno again. it 'just' feels noticably better when driving; nothing huge. but it HAS improved the sound, which was as important a priority to me as the power (i mostly wanted better sound, and no loss of power, then i would have been happy).
i have kept the original centre pipe. i believe it is straight-through and stainless, so is good quality with no impedence of flow or pressure. there is a resonator there, but it does not affect flow. my backbox is also from HiTech mufflers; the smaller 'cannister' makes it fairly loud, but also 'drony' under load at around 2500rpm. i don't mind it, and am used to it. my wife doesn't like it when the drone occurs. but under hard acceleration, it sounds great.
YouTube - Alfa GT 3.2L Mille Miglia high flow cats + rear muffler (1)
quad pipe at the back is a matter of taste, i'm happy with my twin 70mm tips.
anyway, i hope my experiences help guide your choice. i think having straight through rear pipes (no backboxes) would be very, very loud. probably not legal in australia, but might be in SA.