Have you spent much time in either a canoe or a kayak? I find them to be related, but very different. A canoe is pretty accessible. You can pretty much jump in a go somewhere. Learning a few strokes will improve your efficiency quickly, but it doesn't take a whole lot of training to achieve a reasonable level of proficiency, particularly for flat water. A kayak takes a little more practice and training in my opinion. You might also consider a tandem kayak as another alternative.
I don't have enough direct experience to give you any real canoe or kayak based advice with respect to what's better for multi-day trips. However, a comparison with another sport may be useful. One of the things we enjoy about riding a tandem bicycle vs. our singles is that we are always together. When we ride our singles it's often a bit of a challenge to keep together. That may just be us, and a couple that was closely matched in athletic ability may find they can easily stay together and the tradeoffs aren't worthwhile.
And make no mistake, there are probably tradeoffs. There are usually some performance tradeoffs between, for instance, a single kayak and a tandem kayak. You will also find that in a tandem you need to work together. There's a saying in the tandem bicycle world that riding a tandem will either build a very strong relationship, or destroy your relationship.