I always thought that Applejacks parents traveled around a lot. They would travel to all of the different apple farms and just see how things are going. They returned home, AJ's mom is pregnant with Applebloom and stay for some time. At this point Big Mac and AJ both have cutie marks. AB is born soon and they stay around the farm for a couple of mouths and then have to leave again to check out the other farms. Later on they would just die from a storm or falling off a mountain, or just something like that.
So that was my idea why they weren't around at all. They had a job as head of the Apple family. I never did think they were dead.