Now I have to say that while I find this song haunting and lovely - and this rendition of it is particularly beautiful - I still struggle to understand its entire meaning. I do get the Biblical references but some of the other parts confuse me. I was relieved to find I was not the only one who was in this position when I googled 'what does Leonard Cohen's Hallelujah mean?' because literally pages of people asking the same question or trying to answer it came up. The trouble is the interpretations are as varied as those writing them so I decided to simply enjoy it and leave it to you to work out your own meaning/meanings.
It turns out that even finding a definitive version of the lyrics of Hallelujah is not easy but this link gives you a number of variations. Have fun and for some more information here is Leonard Cohen being interviewed about the song.