I can't see the bottom of it on some pictures because there's a wave in front of it. Your experiment is fundamentally flawed because you took the pictures at different times. Have you considered that maybe the waves were picking up as you moved further out or dying down as you moved in, as the case may be?
Thought not.
Imagine this - I take a series of pictures of a ship from 100ft, 200ft, 300ft, and 400ft. I take the 400ft picture at 6:30pm, the 300ft at 7:00pm, the 200ft at 7:30pm and the 100ft at 8:00pm right before it gets dark.
I conclude based on my photographs that the further out I take the picture from, the brighter the ship looks. After all, the camera, lens, and film are all identical in each case.
You see the problem here obviously.
Here's another BIG BIG problem with your experiment - researcher subjectivity. You already knew what you wanted the outcome of this experiment to be. How do we know that you didn't subconsciously time your shutter squeezes so that on the longer shots you'd have a bigger wave in front, and on the shorter ones less wave? This happens all the time in research, which is why we have double-blind methodology. You can be as honest as Gandhi, but your subconscious might still be rigging the outcome.
The only way you can do this correctly is to have several boats out there and take all the pictures at exactly the same time. Given wave dynamics I would imagine that to be within a 100-200ms window, which is easily achievable with amateur equipment. You'll have to correct for the relative altitude of each boat, but I imagine that shouldn't be too hard.
Once you have done that please come back with the new photos and we can get the discussion back on track without worrying about waves obscuring the view. The only thing we are seeing from your photos right now is how high the waves were when you squeezed the shutter.