I have and love the m12 nibbler, and it's a nice tool to have in general. It will work for what you want to do, but will be a little tedious. It really excels for tight curves and tough to access locations. If you're looking to add one to your quiver, and you're using this project to justify the purchase (no judgment, we all do it) I say go for it.
I also have both electric and pneumatic shears, and I agree that is probably a better tool for this particular job if the profile of your decking is the wavy kind vs trapezoidal. If you don't have a shear, and you want one, they don't make one in m12, but they certainly do make them in m18, and of course there are lots of corded options.
All that said, if you're just cutting straight lines, I agree the circular saw approach is probably best, with a caveat. Metal cutting circular saws blades are awesome! There are lots of debates about whether it's safe/advisable to put a TCT metal cutting blade on a normal (wood cutting) curc saw, since they typically spin faster than dedicated metal cutting saws. If you've only got a couple cuts to make, are willing to risk smoking the blade, and are willing to disregard the inevitable warnings that are sure to come, you can probably use a TCT blade in your existing circ saw and make quick work of this job.
If you are in the mood to buy a new tool, I can't recommend a dedicated metal cutting circ saw enough. Milwaukee does have a smaller (5-3/8" blade) metal saw (2782-20), but it's got some limitations. The cut depth might just barely handle corrugated, it will throw chips everywhere, and you will be limited in the thickness of metal you can cut (not an issue for this project but maybe down the road).
If you can swing the cash, I recommend the big 8 inch saw, the 2982-20. It's a beast. It has tons of power, a "chip catcher" shroud/tank that actually works pretty well, and an overload warning/prevention system for when you really want to cut some thick metal. And I'm talking tube, pipe, decking, rebar, and even plate. I've probably pushed this saw harder than was intended, but it's never let me down.
Good luck!