I Since hotel is on the subway line and they will watch your bags for you, I would leave my bags at the hotel and take the subway direct to the city and not have to go to airport twice. The time you backtrack to the airport to deal with storage will take you at least 30 mins. Jumping off airport hotel station to collect bags and back on MTR to T2 just seems so much more efficient.
If taking the MRT from the hotel, I'd have to take the local line. If I want to take the express, I'd have to go to T1/T2 first anyways. At least that's the way it looks on the attached diagram.
