I use the option on the right and consider them to be end plates rather than side plates.
Think Langstroth where the entrance is on the end and the frames are cold way. Now we all have the same perspective, if only temporarily, I'll try to answer your questions.
I use the arrangement on the right and construct the end plate assemblies in a jig using polyurethane wood glue which is a good gap filler and covers for a multitude of sins.
My end plates are standard 9mm, although 18mm could be used without any changes being required to the jigs or the procedure. Like a car, you would not choose to make one of glass, but it does lend structural rigidity to the complete item. Similarly the 9mm end plate is just a rectangular piece of ply that is structurally strong in it's shape if not in it's thickness.
I use the same technique, with a different jig for my 14x12 boxes also and still use 9mm end plates. I don't make SN sized boxes but it's all valid and all boxes have 18mm side plates, 460mm long and the appropriate box height:
460mm x 150mm super
460mm x 225mm SNational
460mm x 315mm 14x12
The end plate assemblies are 424mm wide and butt glued onto the inside face of the side plates.
One side plate being laid on the bench, the end plates stood vertically in position and quickly drawn round to give a guide for gluing.
The end plates are rotated, so that the opposite edge is used to similarly mark the other side plate. At this point the actual side plate mating surfaces are used as the marking templates.
Side plates and end plate assemblies are given a film of glue on the contact areas.
One side plate is carefully placed on battens to give clearance for a couple of
mitre clamps which hold the end plate assemblies square.
I have a thick MDF board, with beveled corners so that it doesn't get stuck, that ensures the correct internal dimension of the box is maintained, and two light spars with notches that fit over the 9mm edge of the exposed side plate assemblies to ensure that they lie exactly where expected.
So currently there is a "U" shaped assembly on the bench, the box on it's side. I present the second side plate, carefully matching up the surfaces to ensure that 3D squareness is maintained (almost).
On top a piece of ply with a large brick provides contact pressure for the glued surfaces and a couple of sash clamps are used over the uppermost side plate to correct any slight tendency to drift out of square.
End plate assemblies 424mm wide + (2 * 18mm) = 460mm. So the box is wide enough internally and externally.
External length 460mm - (2 * 44mm rails) = 372mm cavity length
372mm - 356mm frame bottom bar width = 16mm / 2 = 8mm bee space between ends of box and frame side bars.
Normally leaving overnight for the glue to set completely, I drill two pilot holes through the side plates into each end of the top and bottom bars and screw with 4mm x 50mm screws. A total of 16 per box.
RAB, I could improve my boxes by the incorporation of a drip lip, thank you for the tip.
I would like to build my boxes horizontally on the bench rather than vertically, so being able to use the stone surface to better guarantee the flatness of the boxes which is currently good but not always perfect without a lot of care.
A number of my 14x12 boxes will have the 9mm end plates externally insulated this winter by the insertion of a block of expanded polystyrene foam into the recess on the ends of the box. The results will determine whether insulation is used on the box ends in winter 2011 or not.