Aluminum pop rivets will work fine and you can use the same size. Pop rivets come in different diameters but also different "reaches". You will want a rivet the right depth for the combined thickness of your Royalex hull and gunwale.
To drill out a pop rivet just drill off the large head which should be the part that is exposed. You do not need to drill out the entire shaft of the rivet (usually). Use a bit a little smaller in diameter than the exposed rivet head. The goal is to drill the head off of the rivet shaft without enlarging the hole in the gunwale or the hull that the shaft goes through, and it is usually fairly easily done with the right sized bit and with care.
Once you drill the head off the rivet you can drive the shaft out of the hole (assuming there is sufficient clearance on the other side of the gunwale) with a punch or drift. On boats in which the rivets go through both sides of the gunwales this is a simple matter. On Bell and some other boats the rivets are only visible at the large head end.
Driving the shafts into the interior of the gunwales will leave small pieces of metal inside them which could rattle a little bit. If this is going to bother you, or if there is insufficient clearance on the other gunwale side to drive the shafts free of the hole then you will need to drill out the rivet shafts using progressively larger drill bits.
The gunwales are basically hollow channels that are open at the ends below the deck plates. Conceivably you could get the rivet shafts out by having a couple of people stand that boat vertically one one stem and shake it around. If nothing else, it would make for an entertaining photo op. If you try that (no I never have) first remove all machine screws securing thwarts that go through the gunwales. I rather suspect the loose rivet shafts would tend to get hung up on the ends of the intact rivets, but it might conceivably work and allow the metal pieces to drop out the open ends of the gunwales.
Once you have drilled out the rivets and slid out the seat hangers, you should be able to use a pop riveter to replace the rivet through the existing hole.
Wall Mount Boat Racks
Electric Kayak Motor
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