Transit it simple at DXB and you don't need the Marhaba service. Baggage will be checked through and you won't see it till your final destination. There's always people around DXB to help direct you, so you can easily find your way to the hotel shuttle (someone else should be along shortly to give you more details on that).

While you'll get about half the miles after the entire outbound, that's not enough to upgrade a DXB-NCL (25000 miles). You could do AKL-SYD for 12500 but it's a waste for a 3 hr flight.

Yes, there are different classes - Y is economy, J is Business and F is First, however each of these cabins has different fare buckets where y/j/f are the highest ones - so economy has YERWQKHB etc.

Online check in vs. airport doesn't make a difference. You need to go to the counter while checking in bags and ask for the exit row seat.