I drilled Yakima tracks in my hardtop as well. On the inside of the roof, however, I put some thin steel plate between the roof and the nut to better distribute the load ( I was afraid the bolts may crack the roof). I've only used mine to transport paddle boards but so far so good!

 

Can either rack support one or two 40lb kayaks? That is why I am a little leary of the rain gutter mounts.

 

1 shouldn't be a problem. I'd be cautious with 80lbs up there. Probably be fine, but it might not be. The closer to the edge of the roof the tracks are the more weight it will be able to hold. In a static situation (driveway test) it will be fine. It is when the jeep is moving and the bounciness of the road that I could see a problem. You also have wind from your speed which is putting additional forces onto the roof.

 

I use the Yakima setup with foot pads drilled through the hardtop. I love it for carrying my wooden canoe that weighs 60 lbs or so. I also like how easy it is to remove when not in use.

Once I mounted 2 canoes, 55 and 60 lbs, just to see if it could be done (I had the longer cross bars that gave enough room). I really didn't like it, I just felt it was too much weight, and haven't tried to carry 2 boats at once since. Maybe your kayaks would be light enough to not be an issue, but...

It does generate some noise, but I didn't find it oppressive during a 3,000 mile road trip last summer with my canoe on top. Yakima sells some small noise reducers that clip on the cross bars that may be of use if noise becomes an issue for you.