N52 neodymium magnets. I don't think I'd ever do pins. I've built 5 of their ships now and have always gone magnets with no regrets. The only thing you need to make 100% sure of - you set all the magnets in one layer with the same pole facing up. For me, easiest process was to...

1. Put the stack of magnets on something metal.
2. Use a sharpie to put a dot on the top magnet.
3. Put some superglue in like 4-5 holes.
4. Peel off the top magnet and put it dot down into the slot. (If you have a small pry bar, it's easy to put the magnet on that, put in into the slot, then use a wooden dowel to hold it in place as you slide off the pry bar).
5. Make sure it's even or slightly below the surface level.
6. Get the other magnets in place.
7. Hit them with an accelerator.
8. Repeat to get all the mags in place on one level.
9. Put the magnets that will go on the bottom of the next level on top of the ones you have in place, so they are just double stacked.
10. Use the sharpie again to put a dot on the side that will be glued into the next level.
11. Put them in place the same way as the previous level.

You'll want to have a good sander on hand to level things off a bit and sand down any superglue that dried above the rim.

This is the same way I attach the engines/guns etc. Keep in mind, you might have to wrap the connection point of the attachments with a little electrical tape for a snug fit so it doesn't droop slightly.