Actually it's a mixed bag. A mostly 1/2" system w/ some 3/8" will flow better than an all 3/8" setup, but not as well as an all 1/2" system. (assuming other components are the same, same tubing lengths, etc. of course)
ALL tubing, blocks, etc. has a certain amount of flow resistance, which is a function of the pressure and volume that one is attempting to push through it. This will often be referred to as the 'head loss' or pressure drop of that component. The head losses are cumulative, and the lower one can keep the total, the more flow the system will have.
Head loss is basically caused by turbulence, and turbulence is what makes a waterblock effective at cooling. One of the fundamental ideas is that turbulence in a block will add cooling, but turbulence in a tube doesn't do anything useful. Thus the idea should be to make the water in the blocks turbulent, and the water not in the blocks flow as smoothly as possible.
For the sort of pumps used in a typical WC system, 1/2" offers very low head loss, and essentially is the best balance between low resistance and ease of hookup. 3/8" offers about 4x as much resistance per unit of length. Thus replacing a length of 1/2" tubing with 3/8" will quadruple the headloss for that much length of tubing. In addition, any time you have a size transition (up or down) you get an extra turbulence penalty.
Bottom line is a mixed size system is better than an all 3/8" system, but you'd be far better off if you can get rid of the 3/8" parts.
Building Dual Athlon MP system, Tyan mobo, U160 drives, Server Cube case, Linux ONLY, lots of other goodies. Will water cool, attempting to make as silent as possible.