The animation made me love Pinkie Pie and Apple Jack a lot more , not that I don't lol.
Ehh maybe. Both Apple Jack and Pinkie Pie are earth ponies, and Pinkie Pie once worked in a rock farm whereas Apple Jack currently does her duties at Sweet Apple Acres, but I doubt that means anything about the two ponies' past.
Still, I get what you mean. Granny Smith was clearly telling Pinkie Pie that line. Maybe she meant it in a light way, much like if you tell someone you love them, it doesn't mean you love them in that special way you would for your special somepony. But I wouldn't have a problem if it turned out they were related this whole time.