When we did our home made double glazing we didn't do the portholes. We don't have too much of a problem with condensation on them and the bungs do a pretty good job of keeping it at bay. The other reason is that they're round so it's not so straight forward and we don't have a timber surround to stick the magnetic strips to.
I'd not seen anyone else with a solution to this until today. Andy on nb Festina Lente had come up with a great idea. They have a timber surround on their portholes and he knicked the magnetic strip on the outside edge and managed to get an excellent circle using this method. It seems to be a great success!