Could someone explain the plural form (apple/s)?
No distinction in number in Navajo besides a few nouns referring to people ("boy, girl, man, woman,... "). Plurality can be inferred from conjugation (plural da-, seriative hi-, iterative mode, distributive aspect,...).
Serious question: is this used to reference the company Apple?
Well, it's just how you say apple in navajo. If you are talking about the company, even if Navajo, you would write 'Apple'.