-- Last Updated: Nov-29-12 11:54 PM EST --
I've seen that done too, but naturally it's better to have both canoes flush on the racks.
One thing you can do is put one boat a little farther forward and the other a little farther rearward, so that their side-by-side profile will be quite a bit less than the sum of their maximum widths. It's best to accomplish most of this by rearward shifting of one boat, as moving a canoe rear of center (relative to the rack, not the car) turns it into a "weather vane", while doing the opposite gives crosswinds against the front end a lot of leverage for straining your straps and rack-to-roof connections. You'll even feel your car getting yanked around a lot more with a boat that is positioned forward of center as compared to rearward of center.
Another thing you can do is find a pipe having an outside diameter that will fit inside your cross bars. Using a pipe that's long enough to fit all the way through and stick out both sides will make it easy to anchor in place so it won't slip out. A tight lashing around the smaller pipe just outside the ends of the larger pipe will do the trick (spread the lashing over several inches of the smaller pipe and it will NOT slip). You might be able to extend the width of only the rear cross bar and leave the front cross bar as-is if you position the boats to the rear of center so that there's less overall width on the front bar than the rear bar. You can do a little staggering of boat position too, as described above. Still, for an extra few bucks, you can simply lengthen both cross bars and avoid the need for boat-positioning puzzles.
You could lengthen your cross bars by using four shorter sections of larger pipe that fit over the ends of your existing cross bars, but connecting them solidly will be more difficult. You'd either need lashings that wind both ways (so the pipe can't loosen by spinning) or a set of hooks that grip the outer ends and pull them inward with rope, or drill holes, thread the holes, and install clamping bolts. If your bars are Yakima or something similar, the above method (a smaller pipe running all the way through the inside of your bars) will be much easier.