As a native Filipino/Tagalog speaker, I think that both mean "whole day." I don't think there is a "strict" translation for those words.
When using "buong araw" or "maghapon" in conversations (particularly casual conversations) with us, we would understand it as "whole day." We use it often, and we interpret it as "whole day." What I mean by whole day is from sunrise to sunset.
The word "hapon" means "afternoon." So sometimes, when we hear "maghapon," we interpret it as "whole afternoon" especially if the context of our conversation is about afternoon. But generally, "maghapon" means "whole day," from sunrise to sunset.
There is no "perfect" translation. These two languages have different language rules.