I'm not a lawyer but I do have two of them in the family and I have stayed at a Holiday Inn Express.
If this had been in the US and assuming there was enough probable cause to pull him over for exhaust noise in the first place, then there certainly was enough probable cause to look under the car and take pictures.
Besides, unlike the US, probable cause is not a requirement for traffic stops in Canada. They treat driving as a privilege not a right (actually it's a privilege in the US as well but not to the same extent) so a driver is expected to put up with traffic stops for everyone's "safety". That's why they can do random drunk driving checkpoints that would be impossible (lack of probable cause) in the States.
Umm... Have you BEEN in the US? Random DUI checkpoints have been going on in all 50 states for years, and have been (somehow) ruled 'constitutional' by courts all over the country. Near the Mexican/US border, immigration checkpoints are very common, as well.
OP, I stand by my earlier post- go online (or make a phone call) and determine exactly what code/statute/law you're accused of breaking. This, and only this, will tell you how you should go about fighting the citation.
Be prepared, though, as a favorite in the states is to have a vague law that says it's illegal to modify your exhaust, so pretty much anyone is stuck. Also, they might have a vague sound level law with no db limit- how do you fight that? It's all opinion, and you can bet any judge would automatically side with a cop.
You just won't know anything until you know what you were cited for. Heck, if he did write you for 'no mufflers', then you're fine. Take your own photo, and maybe one from Roush's website, and there you go- they are mufflers. They might do very little, but they ARE mufflers!