"To have the photo come out clearly" means "to get a clear photo as a result". We use "come out (adjective)" when talking about how the end result of a photo looks, especially if there's a process involved.
"Make" means "create" in this sentence.
Science can help with a technically good photo, and art is how the photo can be more than "good", meaning the photo can be inspiring, aesthetically pleasing and emotionally moving.