I would defiantly drain my loop before I shipped it. For one water is heavy, that could really impact the price to ship it. And two, it is a good idea because of pressure and temperature differences especially when it is being flown. O and if for some reason all the movement caused one of your fittings to get loose or something nobody would be there to put a stop to it.
I have also read that using a vacuum on a computer is a terrible idea, although I wasn't aware of why until socialfox's post. Yeah static is a big time no no.
I just built my first watercooling loop in a M-atx case and I've got to say it was quite easy. It's just like building your first computer though. The hardest part is doing all the research. And there is two added steps with watercooling. One is planning, yes you have to plan a computer build as well but with watercooling there are very few "yes or no" answers and there are rarely one size fits all solutions. So you have to be a bit inventive and meticulous. The maintenance is the second added step, I don't see it as that big off a deal at all though, just drain the loop and fill it back up it doesn't seem hard at all. It can be made even easier with proper planning.
Will it be worth it? Depends on who you ask, and around here you will likely get a resounding "yes" Ultimately it's up to you to make the decision. The new 28 NM GPUs put off significantly less heat so there is less reason to watercool but still worth it IMO. and arguably more important than cooling a CPU as GPUs create more heat make more noise and have the biggest impact on gaming. Although with a Sandy bridge-E Processor maybe gaming isn't your priority? And with spending that much on a system there is no way I would recommend against going just a bit farther with a watercooling setup.
One more thing, why not a 690 instead? With a 690 you will produce significantly less heat and power consumption. It leaves more upgrade options in the future, takes up less room, and looks better. It also will cost less to buy one GPU block instead of two. And there is like a five percent difference max between 2 680s and a 690. Which is negated if you watercool and by the fact that a 690 has much much less microstutter, do to a better communication between the GPUs. Anddd you get the bragging rights to having the worlds fastest GPU. I've got the hydro copper edition and it is sweet! It even has the EVGA logo lit up in red on the top which matches the rest of my system.
Read the stickies if you want pros and cons of watercooling and more info on parts. I am sure water cooling has evolved significantly since you last looked into it.