They say they have to be submersed because they usually don't have an inline intake. The intake from the factory is just a grate with a hole going to the impeller behind it. If you have a version of the pump with an intake on it that will accept a hose, it will work fine. The motor of the pump is a design that uses the fluid the pump is pumping to cool it. It will dump a little heat into the loop, but the pump will work fine. Because the pump heats the water a bit, it is better to use this loop:
Pump -> radiator -> CPU -> Pump
A T-line before the pump works well too.
My Via Aqua 1300 was quite loud when I first turned it on, but became nearly silent after a couple minutes. If your pump is really loud when you start it, just give it a couple minutes, it should get quieter. (This noise drove me nuts when I first got the pump, because I thought it was broken and didn't wait for it to get quiet, just took it appart for no reason only to see it was fine)