I played around with various ship and weapon combinations today. In the space of about 10 minutes I lost somewhere around 500-1M credits. The problem was that I frequently used the trade-in feature in the ship yard which basically discounts (depreciates) not just the hull but ALL modules. Had I stripped the ship I was selling of modules FIRST and THEN traded in just the basic/empty hull, I would have lost less than a 100K. Lesson learned. Strip ship of all modules first - as they don't seem to depreciate when sold separately, and only then trade-in your empty ship/hull. Learn from my mistake Commanders! 
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