Significantly slower? No... Try to work some numbers. The pressure drop is half of that of the NB or GPU block @ system flow. Assuming we're using Swiftech's, at 7.2" drop at 1GPM. You're using a Mag 3. Your CPU block is a Swiftech as well, at 8.6" drop. Work out the difference in CPU cooling. I doubt it'll be measurable. Your NB and GPU will both suffer from the reduced flow more than they'll gain from the lower inlet temperatures.
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Erm... You sure about that? If you've got two similar blocks, the flow resistance from them in parallell will be less than that for them in series. While this cuts the flow rate through the paralell blocks, it increases the system flow rate as a whole. If you split the flow at/after the CPU block then surely the CPU benefits from the increased flow while the GPU/NB/Other gubbins (which is less temperature sensitive) has reduced cooling.
This is all theoretical (I have yet to build a water cooled system) but it appears to make sense to me.
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You're correct, although stupid.

J/K, obviously. The CPU gains are small, if measurable.