I doubt it is intentional, more liekly the devs just didn't add code to the arrow mechanics to make them slow down rapidly in water and IG just hasen't gotten round to fixing it or they just don't care about it.

Personally it ticks me of to no end. I've had a few Karves shot out from under me when I couldn't even get a line of sight on the attackers. Then I had to go back and get my gear in another boat with the mobs still camping under my marker. Did not like.