If lua is embedded in starbound - can I write game script that uses standard lua libraries? I.e can I access I/O library and read some information from server file (outside assets directory)?
No - they prevent access of external functions to avoid any user from creating code which may modify other peoples computers. At best you can create your own file with your own custom functions and link to that the way many files use vec2.lua in the scripts folder. Of course with the limitations provided by the game.