Owls have elongated eye tubes that are efficient at collecting and processing light,
which makes it easier for them to see clearly at night.
(A) which makes it easier for them -> "which" modifies "processing light", it doesn't make sense. Incorrect.
(B) which makes it easier for it -> "which" modifies "processing light", it doesn't make sense. and another issue of use second "it" (singular pronoun) for Owls (plural noun). Incorrect.
(C) making it -> Incorrect.
(D) making it easier for the owls -> I find, this is better as, we have "making" modifies the process. Let's keep it.
(E) making it easier for it -> "it" (singular pronoun) for Owls (plural noun). Incorrect.
So, I think D.