Ultra low noise charge sensitive preamplifier
Is it a good way of shielding out a noise?


A faraday cage will shield out just about all E-field noise, and some magnetic noise (not magnetic noise that is close to DC). If the inductor is sensitive to magnetic noise, then you might need a Mu-metal shield (depending on if most of the environments the device operates in has magnetic noise on the frequencies the device is susceptible to). 

Test the shield by generating RF (or hold a cellphone close to the device with the shield on) that will give you an idea of how well the shield works. 


  I was thinking a lot about to separate or do not separate grounds, if
  yes, then which ones?  


A better question would be, is there a reason to separate the grounds? I can't think of one. If the concern is 50V shorting and making it to the 12V rails or the output, these problems could be solved with isolation and\or clamping circuits (on the output).