Don't get too excited. We're not talking just physical nakedness here, but nakedness of the soul. Love, our speaker says, is just a naked shadow. From this, we can infer that her husband was stripped before he was hanged, a humiliating and cruel way to make him seem like less of a man. And his nakedness even extends to the tree, which has been stripped of its greenery so that it can be used for something awful.
Line 4: We may not know that the lover is naked at this point, but seeing him at a crossroads tells us that he is displayed for humiliation at a place where there is probably plenty of traffic.
Line 6: Here, we see an image of the speaker's bruised body, which lets us know that he's probably naked, or at least barely clothed. It's a horror that his dead body is left to hang, naked or not.
Lines 7-8: Besides reminding us of Jesus' crucifixion, at which he was naked, these lines show how naked this tragedy left the speaker feeling about her religion.
Lines 11-12: In these two lines, the word "naked" is used twice. The naked shadow could mean, literally, the shadow of the body against the tree. But it could also be a metaphor for the body of the speaker's lover, which seems just like a shadow. It's a sure thing, though, that these two lines are a metaphor for love. On top of all the metaphor, there's personification in these lines, because even the tree on which the lover is hanged is naked. Trees don't wear clothes, but if our lover were hung on a tree, we'd feel like the tree was pretty horrid and naked, too.