I would push the pediatrician to research for you the dosage of seasickness meds for a toddler b/c as you say, seas can be rough around the Cape.
Make sure you also buy Sea Bands, which you can usually get in a CVS type drug store. They are tight elastic type bands you were on your wrists that exert pressure on a pressure point to counter act seasickness. My kids wear them in rough seas and they help. Also, bring ginger cookies with you since ginger is a natural way to combat a quesy tummy.
Be prepared but also think positively -- you never know! I went transatlantic w/my daughter and couldn't believe it was mostly Caribbean like tranquil waters!
Luisa Frey Gaynor
Family Cruise Editor