I can confirm it is still occurring as of 14w06b. It's not a server issue, it's happening in local games for me, too. The workaround I've found is to quit the game and reload when I start getting close to land. That reloading re-syncs your visual position with the boat's collision box.
I've noticed the same. This is new to 14w06b, it didn't occur in the previous snapshot. I've attached two screenshots to illustrate. The first is a baseline, while standing to the side of the minecart. The second is in the cart. Notice not only the axe, but the sky as well. The clouds and horizon are also darker.