"have an apple" is perfectly natural and has the same meaning as "eat an apple" in the right context. I am very hungry right now. I think I'll have an apple. You missed breakfast? Would you like to have an apple? (I am offering someone one of my apples) You can also use "have" in place of "eat" for things like breakfast, dinner and other meals (as momoxue said). And "have" has a different meaning as well: to own or to hold. I have an apple in my hand. You have an orange. I have an apple.

"have an apple" the phrase is correct on its own. but the meaning is "you have sth" or "sth belongs to you" , and doesn't have the same meaning as "eat an apple". another thing, focus on your usage of "eat an apple", it sounds not natural. Cas, commonly, we say "I'm eatting an apple" " I've eatten an apple", and so on. " have a meal. have lunch" etc. have the same meaning as "eat" them. on this meaning,usually, "have" tents to the whole thing - for example, lunch, supper,dinner and so on. and eat tends to particular object, for example: apple, sandwich and so on. that's it.