1) Would 3 20d nails per stud 16" o.c. be sufficient to hold the
ledger board to the cripple wall, or should I use lag screws? If
lag screws, what size and spacing?

typically, deck ledgers are lagged. i like the fastenmaster ledgerlok
(google). without consulting an engineer, you could put two every 16"
and it would be more than plenty. if the deck is between two walls,
the nails would probably be OK (don't have to worry about it pulling
away from the house), but the fastenmasters are so slick that unless
you need to give your elbow a good workout, I would use them.

if you set the joists on a ledger, you will need to block between the
joists to prevent them from rolling over. also, in actual practice,
getting enough bearing on a 2x ledger is tough unless you are very anal
about your joist length. for that reason, when i have set joists on a
ledger, i have used 4 X material, per an engineer's instructions.
also, you have to prevent the deck from pulling away from the wall
somehow. so with all that in mind, joist hangaring into a ledger is
quicker and easier.

2) It seems like it would be simplest to set the ledger board just
below the bottom of the joists and just let the joists bear on the
top of the ledgerboard. Then I would toenail the joists to the
ledger. The alternative would be to use joist hangers and set the
ledgerboard at the same height as the joists. What are the pros
and cons of each method?

Thanks, Wayne