Watercooling CPU on new rig?

The simple answer to your question is "Yes" it will matter. THe question is whether it will mater to you.

The Corsair H50 is a great solution for a smaller case like the v3 (I know, I have one) because it gives great cooling while not impinging on any components.It will allow you to overclock considerably without bringing up the cpu temp to dangerous levels. That being said though there are many great air coolers that would work (possibly better) and cool at a fraction of the cost.

You just have to be aware of two things:

1. Air coolers tend to be either tall tower like structures or wider "V" or "Orb" heat sinks so you have to be aware of the components around the CPU an how much space you have before you get too close to the awesome little window the v3 has.

2. Air coolers tend to be noisier and more cumbersome than the H50 when you overclock.

Hope this helps!

Air coolers are significantly cheaper and you should be able to OC pretty well on a good air cooler (to answer your question, yes. hydro systems do have a higher theoretical limit). Hydro systems are inherently more complicated and as such, can have problems. While I dunno what type of CPU you are thinking about... or how much of an OC you are looking for... my advisement would be to go with air. Noise is the one downside, so check the db level before you buy.

As far as GPUs, I have never run two cards.

A custom water loop is better than most air coolers, but the H50 is beaten by significantly cheaper air coolers. If you have a tower wide enough for a 120mm tower cooler then i would suggest going for a nice aircooler, you can pick up a cooler master hyper 212+ for about $30 off of newegg, which would give you slightly better cooling for significantly less.