Unless otherwise specified, enemy ships are completely crewed (up to their life support) by enemy NPCs. They do not normally use bots [FAQ]
The referee sets up the enemy ship after the players have set up their ship. Skills and equipment are determined via the charts [p60]. Enemies do not have luck, cannot assist each other, and cannot hold their actions. [YG 335]

The amount of hidden information is up to the individual referee. [YG 588]. Some missions have information that must be hidden. Besides that, stuff to keep hidden in order of added complexity (as noted by Admiral Siadek):

1. Enemy Stats
2. Enemy Power Levels
3. Individual Enemy Locations

One possible way to handle enemies: mark their location, but use a neutral color of markers, so that the players do not know each enemy's profession. [YG 599]