Chris.
I can only repeat, use plugs to hide the nails. If you don't want to go to the expense of buying a plug cutter, just use dowels. For dowels, counter-bore with a 10mm drill bit, and nail or screw the boards through the holes, finally plugging the hole with a dowel. Sheradised fixings at least should be used, but you'd probably get away with any of the rust-proof fixings. For instance, Kreg screws would be fine, and they hold like fury. Over time you will hardly notice the plug/dowel as the cedar weathers, and even if you do, they will look better than the stains. One 250mm dowel will probably fill two or three holes, if you cut them off with a flush saw.
HTH
John