I personally think that you should not repair the crack. HOWEVER, I do believe you should stabilize the crack, because they grow new shell extremely slowly, so a tiny thin repair would just crack again. I'd use some of that 5 minute epoxy, the putty you cut some off and mix it by kneading it into a uniform color. Spread a small bit of it across the crack while holding the shell pieces together. Continue to hold them together underwater until it cures (about 5 minutes, hence the name.) I have some if you need it, but you can buy it at any home depot or lowes for about 5 - 7 bucks.
I personally would not use superglue, because it does exactly what it's supposed to... flow and find the furthest point and glue everything together. Ever use it to glue 2 pieces of balsa or ceramic together? How many of you have had to cut their fingers apart? Guilty as charged. I know I'm not the only one. If you put glue in the crack, it will find the clam and bond it to the shell in an unnatural manner. Don't try to fix the crack, stabilize it so the clam can fix it.