I haven't driven the E with kayaks yet. With the Expedition I had, i didn't even notice them but thats a much different vehicle.
My plans are to haul only one kayak so I don't think the E will notice it much either. I suspect two kayaks may be bit demanding; you may want to consider a kayak trailer instead.
Often when I hauled two kayaks with my Expedition I thought a trailer would have been much easier to load/unload, considering the height of the vehicle.
As for the Thule, its a very nice system. Extremely easier to put on and take off. They also have "rollers" to make loading and unloading the kayak a lot easier. My only complaint is they are sooo expensive.
I don't know much about the Honda rack but I'm going to check into it. Especially if its less expensive than the Thule.
