Yeah, I don't particularly think it matters what gender a child assigns to their toys. I was actually a stickler for canon when I was little, and since G3 had no boys, all my "boys" were fathers or brothers who weren't around (dead, etc.). I couldn't bring myself to make some of my ponies boys, so any males were imaginary. If they made G3 boys, though, I probably would have loved them.
As far as Applejack goes, she looks like a girl to me, whether Hasbro confirmed it or not. But like I said, a kid's toy is a kid's toy, and if they're having fun, it's fine.