Regarding a third day, I'm not sure how often you plan to get back to Cape Breton, but if not sure or the only trip, I would add the extra day to play Highlands Links. What I would do is play 36 Sunday, 18 Monday morning, drive the Cabot Trail to Highlands Links and then play Highlands early Tuesday. Then I would try to add another 18 (if your up for it) at The Lakes on the way south Tuesday. The Lakes isn't spectacular architecturally, but it is a good course, has hosted a PGA TOUR Canada event, and most importantly for this particular trip, will let you take in some great, dramatic Cape Breton scenery as the course works up and down a ski hill.
Regarding flights, not sure where you are coming from but there are flights that go into Sydney, Nova Scotia. In Canada both Air Canada and Westjet fly to Sydney and it's just under 2 hours from either Cabot or Highlands. It all depends on what the rest of your trip looks like, though, as Halifax may be easier if you are doing the Northeast.