Hello Rick,
For (1), it will be HFS, and you shouldn't care. The primary advantage to APFS, apparently, is improvement in performance on pure SSD. The fusion drive, which I also have on my 27" iMac, is mostly a spinning drive.
For (2), just let MacOS install the driver it wants to. It will automatically download whatever it needs from Apple. I have a Brother, but it all works just fine and Apple keeps the drivers up-to-date. I expect it would be the same for your Canon. As to USB 2 v. 3, with your 2 cable, it will default to 2 speeds. Frankly, I doubt you could perceive a difference. With USB 3, you'd just fill up the printer's buffer faster, but it has a mechanical limit to printing, imaging, and paper feeding that is likely far, far slower than USB 2 let alone 3.
For your other applications, sure no harm in checking. To be forewarned is to be forearmed, as the saying goes. If it were me, I'd update those apps that have free updaters and decide individually for the paid apps if I really needed them. I used the High Sierra upgrade as an opportunity for some housekeeping and to throw out old 32-bit apps that I haven't really used in a couple of years (or more).
I am sure you will love your iMac. I find the 27" Retina display absolutely stunning every time I use the computer.
