I am sure there is a more effecient way of doing it but if you go into the DATA/SHIPS/loadouts_utility.ini you can add as much cargo as you want to any faction ship.
Just add a line similar to this to any faction ship and then every one of that ship and that faction should be carrying it.
cargo = commodity_pharm, 1000, hpcargo04

Also .... make sure u shoot aim ur fire @ the base of the transports removing their cargo before they die , this also helps 2 get all the cargo

go into commodities_per_faction.ini, and there is where you can define what commodities are carried by what factions. Remove all the entries for like water, oxygen, etc, and only leave in the high value commidities. You will also have to add in the good commodities to factions that don't carry them. Now their ships will only carry high value stuff (or whatever you want them to carry).

Then, if that's not enough, then open up lootprops.ini, and find the commodity entries and change the last two numbers of the drop_properties. For example:

[mLootProps
nickname = commodity_beryllium
drop_properties = 100, 0, 3333, 1, 150, 150

change the drop_properties = 100, 0, 3333, 1, 500, 500

The last two numbers determine the max amount of loot the ship (or cargo pod in the case of trasports) will drop. So now when you kill a freighter, instead of only dropping a max of 150, it will drop 500! You can raise this number even higher, but the loot will only drop in groups of 30, so if you up it to like 3000, then that means when you kill a ship it will drop 100 cargo boxes! That can really slow the server to a crawl, so I wouldn't suggest that. Of course, you could aslo go into select_equip.ini and raise it so that they drop in groups of say 1000, but that is up to you, and it's a lot more work. =)

Hope this helped!

Yes it did awesome! thanks all.