That is something that still does not fit in my head how it was that they died and to date none of the people who worked in the series said why or what Applejack’s parents died of and what do I know knows what they are deceased for what In the chapter of the perfect couple, Applejack tells Apple Bloom that if they were here they would be proud, which confirms that they are deceased, but what they never explained was how or why they died, and I have two theories: the first is that they died in a accident while delivering apples and on the way there was an accident during the delivery which caused their death and the second is that they died from some disease for which unfortunately there was no solution and that caused them to recover, I don’t know, and subsequently that led to their death from that disease from which they could not recover and that is why they died