I've helped part-pick research workstations with double and triple GPU setups. The case chosen was the Fractal Design XL. The guy who put it together and works with them says it performs well.
So my recommendation is: http://www.fractal-design.com/?view=product&category=2&prod=69
It's not terribly expensive, you can choose if you want the side vent open or not, and it's got a closed top for extra protection from dust or any other material that might fall in. It does not feature a hot-swap bay, but if you seriously need one, I'm sure there are aftermarket solutions.
1. More holes means more noise escaping. With the XL, you can first try with no hole and see if that's enough. If you have no choice but to have the hole, then it's a moot point. The XL has an okay air path if you remove the top HDD cage.
2. No hotswap bay built in, but since the case is not that expensive, relatively speaking, an aftermarket solution would surely be affordable.
3. Water cooling has noisy parts like pumps that you'd have to modify to get silence. The prebuilt kits are also not that powerful. To quote an SPCR review
: "The Kühler H20 620/920, even though they have quieter pumps than the H50, are still handicapped by the additional noise source of the pump, making them impossible to succeed as super-quiet CPU coolers. [...] For performance oriented silencers, stick to tried and true air coolers. They are both cheaper and more effective.
4. XL has intake filters.
6. XL supports E-ATX.
7. There is a lower cage that can fit up to 6 drives. With 3 you can have sufficient space between drives for effortless cooling.
8. I haven't seen a Lian Li I thought was worth the asking price. Only if you absolutely must have some feature or design should you pay their level of premiums.
I have seen one case where a user complained of vibration issues, but they had a 7200 RPM WD Black to begin with. With the right parts I'm sure there's no problem, as I've seen more satisfied cases and only one with any sort of complaint.