Good, at first looks like you were a bit unlucky and got the wrong link, yours is about the NPCs not about the Player Faction, here is the correct one CR Disco Wiki Linky . (Factions /Houses not mentioned are to be seen as neutral)
And as it seems just one person chased you down the whole way, that isnt much effort for a strike against slavery and the drugs, or? Its one of our ships for a ship that may damage the life of thousands.
And for the Nyx, its an old topic, the Nyx was designed when Colonials still used the IMG IFF, thats why it got the IMG-ship Infocard. But since 4.85 we got our own ID and IFF, so the whole Nyx/Pytho/Hydra/Argus/Zephyr = IMG thing wasnt needed anymore. To answer your question, we just try to get back what was originally made as ours. These things should be solved in the new Mod.
Its a bit sad to hear that you never had a nice experience with us, but we have to face those silent "I TRY TO RUN AND SAY NOTHING" Type of Smugglers far to often, which can be really annoying from time to time, you have to understand that if you try to Play your role and get nothing back then a person launching the cruise engine again and again is a bit frustrating... Sometimes it helps to think about how the other person may feel about it :P
Try to Say something and who knows if you are able to bring a good story the Colonials may even let you leave with your cargo.