Cargo bays do what they say on the tin; they store your stuff (or other people's stuff, mostly other people's stuff). In order to carry trade goods, collect the juicy exotic matter from the exploded reactors of that unwitting trader's ship or store that pirate's possessions which you redistributed to yourself. Generally the more of these you have on your ship the better as you can either carry more trade goods to make routes more profitable or carry more loot from destroyed pirate or SSC ships.
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