Hemingway's "The Old Man and the Sea" is a classic example of man's stoic resistance against the cruelties of merciless sea and nature told in a simple yet forceful and lucid language. Here man is pitted against nature, youthful energy against elderly endurance.
It appears that that the sentence can not be reworded as the aloofness as well as the intensity captured by 'empty it' would then be missing.
It is an example of extraposition. IT is the impersonal pronoun which function as extraposed or postponed subject. IT has many an epithet added to it— empty, artificial, dummy, introductory, provisional or anticipatory. However, we would call it 'Provisional subject'.
"It made the boy sad to see the old man come in each day with his skiff empty and he always went down to help himcarry either the coiled lines or the gaff and harpoon and the sail that was furled around the mast."
This sentence should not be regarded as a cleft sentence which is often filled by an 'expletive or empty IT'. But this is not the case here. In the extraposition as above, the clause begins with an IT which is cataphoric referring to a clausal item which in our case is a non finite one ( to see the old man... empty). Here the theme position is occupied by cataphoric 'Pro IT'; it is semantically empty but this extraposed version is more natural according to Quirk et all and more so specifically when the name phrase that follows the dummy "Subject IT" is longer than the complement and is better placed at the end of the sentence (Downing & Locke).
One last word. Extraposition is more common when it relates to thinking about or evaluating the situation or mental process. Call it a Cataphoric IT/ an example of extraposition.