"A" buses services, commonly called CityFlyer are predominantly used for regular passengers to/from the city. They are operated by CityBus and for sure they'll use a bus with luggage racks on this line:
link. Even if one bus is under maintenance, they have a large fleet. You'll have no problem with your luggages. Some locals, like my mom would travel on it with a lot more luggage than that ;-)

"E" buses are usually a bit harder to find (usually more at the back) and are predominantly used for airport staff and airline crew. It will go through airport office buildings and Cathay City, to pick up staff. "E" buses are cheaper but since it makes that detour, it also takes longer. I'm not sure but "E" buses should also have a few luggage rack, since it's used by airline crew (and passengers who wants to save a few bucks).

My advice if you're visiting HK is to use the regular "A" bus service. You'll be more comfortable there and it's more designed for visitors with clearer signage and indication.