You'll know if the boat is taking on water when you have it on your dolly with the plugs out and the bows raised up in the air. My boat generally does not take on more than a few ounces of water during a sail of 2 to 3 hours.
The mast should be leaning (raked) back. Some Hobie 16 sailors take great pains to make sure the mast leans as far back as possible. For boats with a lot of mast rake, when the boat is sitting level, and you use the main halyard as a plum-line, it will hang down near the rear crossbar of the tramp.
If you don't have a significant amount of water in the hulls, my bet is that you and your crew just need to shift forward. In lighter wind you will both want to be up near the front cross-bar to bring the sterns out of the water. The Hobie 16 sails fastest "on it's nose", so keep your weight forward as much as possible. As the wind increases, and the increasing power drives the bows down, you can start to move back to prevent a pitch-pole.
Hope that helps, and happy sailing!