no you're not nuts. The bottleneck will create a pressure difference (higher before, lower after). If this does not affect the pump (it will), the water would flow at the same rate. Since it does, your flow will drop slightly depending on the pump.
If you are using very small pump (120gph area) it will cause more of a problem. Unless you have a
Also I believe the length of the bottleneck makes a difference. IE, if the bottleneck is a small fitting the flow will be reduced less than if the bottleneck is a section of hose. 'sub-bottlenecks' can hurt flow too... IE if you reduce to 3/8 and then have curvy hoses or T junctions. Such things work better with large diameter.
For the first question, high flow GPH is good, but high velocity is not as important. Hi velocity would only be required if the water was colder than ambient in the tubing and you wanted it to get to the waterblock ASAP... this is only the case if you have a REALLY REALLY hot case or are using some kind of chiller. Even so, the gain you might get with high velocity might be offset by low flow, so stick with the larger diameter whenever possible.
Also increased pressure at the block is only good because it means more flow... increased pressure would help with air (denser air absorbes more heat) but not with water (same density when in liquid state)
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