His reasoning for cutting her hair went beyond pranking and jealousy. He wanted to see if Thor was as fickle as he suspected him to be, if he would still love her without her beauty, because if he didn’t, then Loki would be waiting for her with open arms.
He was disappointed, of course. Their love was as strong as ever, and Loki remained alone. He still loves looking at Sif and her black hair, though, knowing that he put it there and that she accepted it enough to not force him to change it back to blonde.
He also kept a strand of the gold hair, which is tucked in one of his spellbooks to this day.