Although we did not see any mosquitoes, we were told that we should take malaria pills. You should also make sure your vaccinations are up to date for travel in Indonesia. Our experiences while there were remarkable because they were offered through the hotel that we were staying. I would highly recommend the Komodo Resort Diving Club. We snorkeled and did the land excursions offered there.
It was hot and humid in March, but the boat offered lots of cover to avoid the sun. It did not rain while we were there, but it is the tail end of the rainy season. Bring lots of clothes that will dry quickly and make sure you have a sun shirt for snorkeling in the water. All food is included in the cost of your hotel stay. However, for all boating and other excursions you pay à la carte.
Early morning is cooler for hiking, but it doesn't really matter. Everything is available to see or do all day long.