Shot in the dark.

[NoNickProvided]

This is just a shot in the dark but your game seems to be acting exactly like it has these two problems:

Unity does not cleanly destroy gameobjects when you call GameObject.Destroy(). I do not remember if it was the mesh or the collider that caused the problem but you can help your growing memory usage by adding in an extra Destroy() or two hitting the gameObject.collider and .mesh before killing off the actual gameObject.

Again it was either the mesh or the collider i cannot remember off hand but there have been many posts about it..

Second creating gameObjects is a violent process but re-purposing existing ones is not so much. The lag you get when trying to place large pieces on a large ship might not exist if you did not have to spawn them/ that many at that moment. Creating a bank of say 50 gameObjects with the nessesary components attached at loading and just leaving them sit and wait to be used if there is call and only creating a new gameObject in an emergency or idle. Then if parts of the ship are deleted do not delete the gameObjects for them just null out what you do not need anymore and add them to your bank..

Anywho idk how you actually do things but you use unity and these two things are pretty common and your game appears to have issues with it.

[Xaiier]

Um...ok...

A few suggestions to improve your posts in the future:

• Reference the issues you speak of with sources and information, so that we can validate your claims.
  
• Take the time to understand the internal processes of the game before making vast assumptions about how it works.
  
• Explain in detail your "issues" and provide valid proof that confirms that your ideas would work to solve them.
  

[raidernick]

Um...ok...

A few suggestions to improve your posts in the future:

• Reference the issues you speak of with sources and information, so that we can validate your claims.
  
• Take the time to understand the internal processes of the game before making vast assumptions about how it works.
  
• Explain in detail your "issues" and provide valid proof that confirms that your ideas would work to solve them.
  

Didn't you see his name? NoNickProvided, that also means no explanation or proof provided either.

[Kermunist]

Well, here's a source for the first problem. Though perhaps it would have been better for the OP to provide it.

http://answers.unity3d.com/questions/9999/procedural-mesh-leaks-memory-everytime-the-game-ob.html

note who posted the most recent comment on the answer. Note also the dates, this may well be fixed in Unity now.