Honestly just saw 苹果 a couple days ago so even that spelling can't be called that rare. It really depends on what you're consuming, if you're just reading daily SoL content I doubt you'd ever see it but I do think 林檎 is pretty common.
I have not seen 苹果 before, where did you see it? It looks Chinese, and Japanese Wikipedia calls it "簡体字中国語表記". I don't think most native speakers can read it!
Outside of Chinese (where it is standard), I’ve not seen 苹果 before, but the Japanese input on iOS suggests it after a bit of scrolling. It’s in the dictionary on there as well, where the pronunciation is given as ひょうか or へいか, which is fairly logical.
