You are correct, at home the armour is removed. The kit Trumpeter does have the bolt on armour molded on, but it also includes un-armoured hatches (listed as 'not used') so you are some way towards de-armouring it. It also has the correct pattern hubs included. As for the exhaust, it's pretty easy to mod, and if you get one of the Stryker PE sets, they come with the correct shaped mesh grill, so you can use that as a template, and add it to your scratch built exhaust and your good to go.
Be aware that on deployment to Afganistan, the Kiwi LAVs are fitted with the suvivabliilty kits from the LORIT upgrade, including the turret and rear hull armoured screens, the belly armour kit and the front hull mounted spare wheel bracket.
Currently there is no from the box answer to either of these. I'd stear clear of the Black Dog LORIT set, while the stowage is fantastic, the add on armour screens are terrible, and mine came with the front spare wheel bracket broken into several pieces. I've got the Real Model LORIT conversion for the trumpeter kit on order.