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No it does not matter whatever way uses less tubing.
 

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The only components where flow direction usually matters are:

CPU blocks
GPU Core-Only Block

Both of those components often use jet-injection plates that force the water to act in a turbulent matter, increasing performance. If the water was pushed through the other way the water would not pass through the jet plate first and thus would not be forced into turbulent flow to the same degree.
 
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