How can I counteract for any movement caused by surface waves when instrument is mounted on a boat?
If you are planning on using a boat/ship to take profiles, then you may want to put it in XYZ instead of ENU so that the influences from the hull, engine, etc. do not influence the profiler's internal compass. Instead use the ship's gyro. If you boat is non-iron then you should be safe as long as the profiler is away from the engine. The option of making the measurements from a buoy may be a better bet. There are less influences from the ship with regard to compass and currents.
Surface waves effects
Surface waves will effect the current measurements; the good news is that you can rectify this.
The first issue is the local currents created by the waves themselves (orbital currents under a wave). These local currents have the same period as the passing waves, and the mean current over one cycle is zero. This means if you average over one cycle then you will remove the wave induced currents and be left with the mean currents which is what you are most likely interested.
The best way to average out wave currents is to select an average interval that is long relative to the expected wave period. If you expect waves to be no more than 10 seconds then you will be fine with the default average interval of 60 seconds.
The second issue with surface waves is the motion of the buoy/profiler. The effects of changing tilt and heading can be accounted for by sampling the tilt and compass sensors faster. This is exactly what is done when you select the Buoy Mounted option under the mounting choices in the Deployment planning. As long as the buoy is not violently dancing on the ocean surface, the measured orientation may be used when we convert from beam coordinates to ENU coordinates. Furthermore, by averaging over a duration of 60+ seconds will help remove any bias created by motion of the buoy.