That is a good question, as I haven't used the boats in ages. I typically go to the parks like an every day guest, or if I stay on property I just walk there, which in both cases one way, or another you do go through a security check point.
However, I just checked online and on touringplans' blog, they say they are currently working on permits to install metal detectors in the boat dock areas. Do not know how much of a reliable source they are when it comes to that sort of information, however, due to how secure they've been trying to make things in CityWalk/Universal and using common sense, I would imagine it is happening, if it hasn't happened yet.
I do not know how much "faster" things will be, as last time I went through security it looked just about the same. However, it will be more efficient in the sense that it's going through a machine in one motion and not relying on people to check and double check while fumbling through all your stuff.