I can't hear the 40mm fan over the 92mm fan that comes with the Supermicro drive bay. That fan is louder than anything else. You're 100% right that this case is well ventilated, but also not well insulated for noise. A few pieces of noise dampening material would be useful. The 40mm fan is rated at 3500 RPM, 4.11 CFM and 14 dBA if that helps at all.
I have a fan that I want to buy on auto-notification from newegg that will replace the noisy fan in the supermicro, but I have to live with it until then. The NAS is in my office room right now and I can't hear it anywhere else in the house. I also haven't been leaving it on 24x7, but will eventually put it in the basement or somewhere out of sight.
In my short comparison between freeNAS and openfiler, I like the UI usability of OpenFiler better than freeNAS, but the features seemed comparable. I also had hardware compatibility issues with freeNAS which made me move back to OpenFiler. My hard drives were disconnecting with the onboard nvidia SATA controller. Now that I have a Perc in here, I should try and go back to freeNAS to see if it even recognizes the controller.
With OpenFiler, I was also able to easily update all the rPath packages using the built-in update mechanism which I find very handy. When they come out with improvements for compatibility and performance (as was the case with their iSCSI software), I can easily get the conary package from their rbuilder project.