According to jpdb possibly the only visual novel with the spelling and to be honest it was in an excerpt of a translation of a play, and it had furigana. :p https://jpdb.io/vocabulary/1555480/%E8%8B%B9%E6%9E%9C/used-i...
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.
林檎 for sure is common.