On Cable style lifts you can leave bunks out of the water. You also end up with less cable in the water if cantilever style lift.
On hydraulic lifts, they recommend leaving them down otherwise you build up a layer on the rams at the water level. This results in potential damage to the seal unless you clean prior to use but sometimes they will pit and it will still damage the seal. I sell Hewitt lifts and still learned the hard way. Hewitt recommends hydraulic lifts to be lowered as much as possible so the least amount of ram (chrome portion) is exposed.