The Dune products may do the trick. This is why I actually bought a Dune. It was one of the few (only?) players which supported Blu-ray ISOs with the full menu structure as I have converted my entire BD collection as a 1:1 copy onto hard drives, and it supports about as much storage as you want to throw at it. I have 10TB sitting locally attached, and it can support network connected drives.
According to the FAQs, it supports FLAC up to 192/24.
http://dune-hd.com/firmware/hdbase3/
Yes, people regularly run Blu-ray over media servers or NAS drives. You've got some good options there.
I believe you can either internally decode it or bitstream from the Dune without issue. My DVDs were no problem at all, Blu-ray hasn't failed on me, but it is definitely slower to load, as Blu-ray players themselves often are.
Nope. This is my biggest headache with the Dune. It is stable, but doesn't support a bunch of other stuff. I'm really hopeful that they will open a market of some sort to allow end users to develop apps which are great.
Ditto on this to the above.
One of the best things about the Dune is that it seems very stable. This has been an issue with a lot of other players which I keep reading about. Documentation with the Dune is weak and it takes a bit of technical know-how to set it up the first time. But, once you get the setup done the actual use is easy. Zappiti provides a nice GUI for your movies as well.
I'm hopeful they will come out with a far more powerful unit than the ones they are currently using. It would be nice to get these with GB interfaces and some serious processing power along with the reliability and stability that makes them easy to use.