I have never seen it either but its an intriguing concept. As mentioned, I have seen people slide their kayak through the front bunk on the old style bunks like mine.
But, I think you want to answer a few things for yourself. I'll list them off and they are not meant to dissuade you; just items to consider...
The roof can handle the weight. After all, we climb up there. But can it handle the stress at the connection points?
Will it void the 10-year roof warranty?
I would not add a ladder to the back of the Roo. Not sure how this would work with the bunk end and so on.
So, how will you get them up there? I'm really used to heights and climbing but that seems like an awfully bulky item to move up there solo. I think it would require a second person and maybe that is what you planned.
Consider the increase in the overall height of the trailer. Maybe this is not an issue because I imagine the kayaks would lie flat and still be below the AC cover.
Consider double-towing (or "triple-towing" if you prefer that term) if you live and camp in an area that allows that and you are comfortable, which I am not particularly comfortable.
Finally, take two vehicles instead of one. That's what most of my friends do.
Let us know what you decide!
DW, 3 Kids and our Goldens
2012 Shamrock 233S
2008 Toyota Sequoia 5.7L 4WD