I found out where the game spawns the hidden ships and crates. It is in the script "3.08 Sector Management.pck" near the end of the file.
For crates the game spawns eight, either engine tunings or rudder tunings. It spawns 2-5 each per crate.
As for ships it seems you can get: one of: 100% - Kha'ak M6 with default loadouts any mix of eight of: 30% - Kha'ak M4 or M5 with max loadouts 70% - Kha'ak M4 or M5 with minimum loadouts any mix of four of: 30% - Eclipse Prototype or Mercury Prototype or Demeter Prototype or Advanced Perseus or Enhanced Dolphin or Enhanced Mako or Enhanced Chimera or Scorpion Prototype or Toucan Prototype or Falcon Prototype with max loadouts 70% - Kha'ak M3 or M4 with max loadouts two of: 30% - Kha'ak M3 with default loadouts
I didnt bother to decipher the sectors, as they are pretty random and it wouldn't help much
Ищите еще контейнеры - я вообще, пока, ни одного не нашел.