How long is your trip again? If 7-8 days, be careful not to spend half of those days getting from one place to another and not having much time being somewhere (same advice as is often given to folks planning fast-paced trips to Europe).
Getting between Vancouver and Victoria shouldn't be difficult - besides the direct ferry, there are huge car-ferries that you can connect to via bus.
Is several hours enough to explore Victoria? I wouldn't think so. I can easily spend the better part of a day just in the museum there. The city is "cute" (purposely so) and I'd think worth more than a few hours.
I don't think it's reasonable to take a long ferry from Seattle to Victoria, just spend afew hours there, then take another ferry (3 hours+) then go to Vancouver....that's a lot of time in transit.
To your specific questions...
1) if the two ferry rides will be very different scenically, or if the Seattle-Victoria ferry will give us a good feel for the Pacific NW Islands
Both ferry rides would probably be pleasant for someone who has never been here. Not what I'd call spectacular, though. You will see some coastlines in the distance. Some of which will be islands, some of which will be attached to the mainland. The coastal scenery, while certainly pleasant, isn't especially stunning. You will see more coastline (mostly in the distance) on the ferry between Seattle and Victoria (its a much longer distance). The ferry between Victoria and Vancouver is mostly open ocean (technically it's not "open ocean" but most of the time it's distant from any land - you'll mostly see water. Both ferries will thread their way among some islands, which are pretty, but it's not exactly the Amalfi Coast either. From a distance, most of the coastline/islands you will see will probably look pretty similar. Don't get me wrong: the ferry rides are relaxing and pleasant (if it's not raining), but they are not what I'd call breathtaking - its a lot of the same. A nice way to go, but takes some time.
1A) It might be very cool to fly between Victoria and Vancouver.
No, there's no "might" about it. It is definitely very, very cool to do this - THAT is the best way to see the beauty of the area and the view from a small plane is stunningly beautiful (I fly over this area frequently, did it last weekend, it's always great). Be aware that the planes used for this are very small - if you are skittish about such things. But there's no better way to appreciate views of the area's beauty. If you can manage the cost (and you're not spooked by tiny airplanes) this is the way to go. Really.
2) Does Victoria merit staying overnight in any case? Or is that additional night better spent in Seattle or Vancouver?
It seems crazy to me to go to Victoria and not at least spend a night (or two, actually).
Bonus question: If we go by air, should we do the helmet or the plane?
??? Unless you've found some new service in Seattle that will fire you out of a canon pointed north, I don't think you need a helmet for any flights to Canada. A barf bag, maybe, but no head protection required.