I have magnetic hatches on three kayaks and I like them a lot. Like any good hatch system that is well constructed, they do not leak. They are so easy to remove and replace in their watertight position that my paddling partner can get something out of a compartment for me between waves. On long paddles we often put lunch or a spare coat right under the hatch because we know that we can get at them quickly. Also, there is no risk of departing with the hatch in place but not secured. Put them close and they snap into position.
Installing these hatches must be done just right, however. The fit must be good and the gasket must be thin and very compressible. Magnetic attraction falls off very rapidly with distance, so you must get them very close together. The rare earth magnets corrode very easy, so they must be sealed under a layer of fiberglass. Merely coating with resin is not good enough. 3.25 oz cloth works for me. The magnets are so strong that they will pick up sand and small gravel. If you leave this debris on the magnet, it could perforate the resin seal and the magnet will self destruct with corrosion. If you paddle in a very sandy place, magnets may not be a good choice.
The magnets I used are 1/2 inch in diameter and 1/8 inch thick. I used 12 to 14 pairs per hatch, spaced about 2 1/2 inches apart along each side. They are installed so that they are flush. It's a bit tense drilling holes in the hatch lids so I used a drill press to keep from drilling all the way through. I bought two cheap forstner style bits to do the work. The first one was used normally to start the hole. I ground off the center point on the second one and used it to finish the hole.
These hatches have proven to be secure in all of my paddling. They have passed the test of rolling the boat with loose gear inside more than once. However, I do have an alternate way of securing the hatches on both boats. On the Tern I have plastic hooks the allow me to stretch a bungee over the top. On the Silver and King I have an under the deck adjustable leash which is cleated in the cockpit (see photos at bottom). I secure these hatches when the boats are on the car and in rough water. The thought of losing a hatch on the highway gives me the willies. I have forgot to secure them more than once though while on the highway with no problems.
Compasses mounted too close to the magnets will not work well. Clearance of 18 inches or more should work out OK though. When I tested for interference I found that the rebar in my cement floor had more effect. I alternated the polarity of each pair but I don't know that it makes much difference. Magnets mounted with the poles horizontal (vs. vertical) will have a large effect however. This rules out using magnets to hold on a removable bulkhead. If you want to have some fun with someone else's navigation, carry a stack of these magnets in your hand and watch what happens.