Online check in at t-48 usually works well. However, on booked out flights it is useless. So if you travel on Chinese national day or around Hong Kong public holidays, the seat selection may be disabled/all seats taken at t-48.

I've noticed that tickets bought through expedia.com.hk for ex-HKG itineraries allow a seat selection at purchase of the ticket (no extra cost). That is valid for core economy booking classes and fare buckets (incl. S and N). I'm able to "prefer" a specific seat (e.g. 39K). The preference is also visible on Cathay.com my booking. So far I've also gotten that seat at check-in.