Here is a photo of C pup, at Catalina Island 2012 gathering. He has as much "stuff" on a C D 16 as I have seen. I also saw one which was starting from Seattle area, with the goal of getting to SE Alaska. So these little boats certainly can do a lot more than most 16 foot open boats do.

The beam of the 16 is 6'6", but it is narrower at the waterline, as most semi dories are. The C Dory 22 has Beam of 7'8"--same thing about the waterline beam. We often carry a light weight dinghy--about 55 lbs on the cabin top, There is a slightly noticeable difference in handling.
If I was towing a Kayak, I would put a towing eye on the boat. Although I am not a big fan of towing in rough water, I have often towed kayaks, small and large inflatables up to 13 feet, an Aluminum 12 foot boat, and even a 20 foot walk around Grady White. In each case, I put in a specific tow eye. If you are going to leave the kayak in the water along side the boat you will need attachment points. We are going into the kayak rental business in a State Park, and each of these will have at least two additional strong points installed in the kayak for security and possible tow reasons. You put in a backing block, and drill the holes for screws or bolts thru the hull of the Kayak.
The issue is not just raising the center of gravity--but of changing the characteristics of roll in heavy seas--and though it is not obvious--there are differences dynamically between raising the CG by moving batteries/ and even people in the lower part of the boat, than adding 50 or so pounds on the cabin top. Another issue to approach is getting the Kayak on and off the rack--especially if the boat is not on the beach, and floating in deep water. It certainly can be done, but we use a Davit on most of our C Dories to move even the inflatables to the cabin roof.
Part of this is the weight of a person on the side deck, and then the boat heeling more because of this and the weight of the kayak. It is not going to tip over--but may be a challenge.
No one means to be chiding you--and I believe we collectively feel sorry if our comments came across that way. It is easy to put a couple of foam pads which are made for putting a kayak on a car top, and trying it out--vs putting a rack up there. Walmart carries an"Atwood" foam block set with straps for $20--you might consider giving this a try, before investing in the rack.
Regards,