Not basing this on anything that has been said at or about Monzo, only Wirecard and Apple but I don’t think you’ll see Monzo in Apple Pay until after current accounts launch in 2017. At the very least, that is where I would put my expectations.
Otherwise, it’s quite a lot of integration and paperwork to do and then have to throw most of away to rebuild when the Monzo service moves from being a prepaid card to a full bank. Even if Apple Pay and Android Pay cards with their tokenisation is the end goal for both security and speed/cost of opening a usable account.
I do feel your pain though, it’s always a difficult choice between using my Monzo card or Apple Pay. A decision that may be getting harder very soon with new Wallet functionality. 
I generally go Apple Pay for contactless above £30, Monzo for chip and PIN or below £30 contactless right now.