The idea of an "L" assemble along the sheer makes me think it'll capture dust, dirt and most importantly, moisture, just under the deck, between each beam. The sheer clamp, a hardwood 1x2, (vertically oriented) glued and screwed to the hull shell along the inside of the sheer, is all you need. Outside of this and also screwed to it will be the rub rail, which just adds more beef in this area, you don't need a horizontal oriented shelf.
So, if the rub rail is 1" thick, the hull say a 1/4" thick and the 1x2 sheer clamp, brings a total of 2" of material along the rail at the sheer. That's enough heft to bash things pretty good and also accept fasteners and glue.
If you'd like to avoid the sloped pockets in the sheer clamp, just notch it, very slightly, say about an 1/8" deep with a router and a flat bottom bit the same thickness as the deck beam. Just plow out this shallow groove at each point the deck beams land. When you fit the deck beams, they'll "key" into the slot, but you'll need a heavy structural fillet on each side (beam to clamp) to hold it in place, as well as the epoxy used to glue it in the shallow groove. The shallow groove just locates it where it needs to be and is slightly simpler then the sloped joint I've shown.
You could also skip the shallow groove thing too and use just plain old wood working, such as a knee. This would be a horizontal triangular piece screwed to the beam and the sheer clamp. It seems a simple thing, but the topside angle the sheer clamp is at, has to match the slope of the deck beam in all three directions, so some fancy cutting will be needed after "picking up" the bevels with a gauge. Naturally, you'll probably want to epoxy these into place too.
Lastly you could employ just straight "liquid joinery" techniques and use only a structural fillet on each side of the beam/clamp interface (use the 3:1 fillet radius rule). Technically, this would be okay, but I'd still be tempted to place a big old honking screw in, through the hull and sheer clamp, into the end of the beam, just to be sure it doesn't move. Call me old fashioned, even though I know the epoxy works by itself, I don't trust it all by itself except on fairly small boats.
On the aft deck treatment, I wouldn't have but a little chunk of aft deck. On small craft (I know what I said in the last sentence of the last paragraph) I've found you need to occasionally get at the transom, to reach over, fend off, smack down boarders, etc. With an aft deck, you have to climb up on top of the thing, hope to not fall off and tend to whatever duty has demanded you get out on that dainty, sparse handhold area. Me, I'd rather walk out, lean over, grab whatever I'm after, then go back to the cockpit, reasonably upright, as I've found I'm more secure upright then on my knees. In the case of your boat, I'd curve the aft end of the cockpit, so I could get to the center of the transom in arms reach from the cockpit. It could still have the aft deck thing I know you like, but the curve will let you get closer to the transom if standing in the center of the cockpit (or kneeling on that seat). It's a personal taste thing I suspect more then anything, so do what you like, I'm just throwing around options.
