I would stick with the screws.  I installed mine that way and added fillets along the bottom of the trunk on the inside of the hull.  

You'll never know they are there. I'm sure you could figure out some way to clamp it but what if it gets crooked?

I too was concerned about encapsulating screws, but other builders said that was the better way to go, so I did, just dont let air get trapped on the screw heads when you epoxy the bottom...but I did also use this clamping method from the manual:

 https://picasaweb.google.com/lh/photo/nZ_Xfj2DNGjSBv_STshCZzFolq1y-t7pqfyiNmzJPv8?feat=directlink

And also 2 screws thru the bulkhead to suck that up then put the screws in from underneath into the trunk

The sequencing of the steps here are important!  A lot of back and forths for alignment, pilot holes, then buttering the mating surfaces then screws.

  You're sailing around passing the beach and showing off your beautiful boat when suddenly the daggerboard snags the bottom.  You didn't use screws and as the bottom of the daggerboard moves astern the top goes forward and now you have a very large hole in the bottom and instead of all those bikini clad girls clamoring for a ride, they're laughing because you've sunk up to your neck and your hat's floating away. You had your ID in the hat and when the marine police arrive to investigate the report of a sinking you don't have any ID and can't prove you didn't just come from Cuba so it's off to jail where you're put into a cell with Bubba.  You made the mistake of telling Bubba your sailboat just sunk without knowing his girlfriend just dumped him for a sailor.  Don't get put in a cell with Bubba. Use screws. 

Dale's right---the epoxy along really is strong enough in theory.  In practice, it's possible to give your daggerboard and trunk a gigantic wallop if you hit something hard enough.  It's one place where I think the belt-and-suspenders of fasteners AND glue is worthwhile.  (Also on the mast step, and for the same reason.)

Just countersink the screws slightly, plug the holes with thickened epoxy, and worry no more.

I used to use screws on my Y-Flyer center board trunks. Epoxy over the screw heads.  I cannot ever remember having a problem.    

Here's an alternate point of view -  screws make the joint weaker, not stronger. The holes and threads cut and tear the wood fibers. When taking that gigantic wallop, the sharp threads act as stress concentrators (or knives) and chew up the wood. The wood and metal react to temperature changes differently. The metal expands and contracts more, working itself loose and providing a space for water to enter. As it expands, the screw threads are driven deeper into the wood fibers, chewing them up even more. If the screw corrodes, it can spall and expand, again widening the hole.

As a practical matter, it probably doesn't make any difference, otherwise the forum would be as full of people posting about joint failures as it is with people asking about crystallized epoxy every winter.

But not putting sharp bits of metal into a joint is my belt and suspenders.

Have fun all, winter's 1/2 done.

Laszlo