Can't patents be filed by a shell company? This possibility is abused by patent trolls.
It is obvious that the patents were in first place given so that the inventors can safely claim their inventions without them getting cheated of the royalty/credit and any profit earned from their work. This obviously is not possible if the patents are granted anonymously. Then their is also the issue that patents are quite often challenged on their rights of ownership and the judiciary cannot effectively deal with anonymous clients.
This is also only when you are applying for a patent as an individual. If you apply as a group/company/university than your patents are granted under that particular umbrella.
That being said, it is worthwhile to remember that patent laws have been abused many times in this respect. Patents can be given to groups that part of even larger groups and so on. This means that the 'larger group' can still stay partially anonymous.
Well, let's say you file a patent anonymous. Then how is the government going to verify the real owner of that patent? Because anyone could claim they are the owner of the patent.