In the article I noticed this line. Does that mean that only people who received this ship by chance rather through the exchange can receive the hanger pet if they wanted it?
Yes. If you currently own (whether you got it from the exchange, winter package, a DOFF pack promotion, etc.) the attack ship and the dreadnought, you can obtain attack ship hangar pets.
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My question: will you guys add the new Dominion ships to the enemy mobs and the Foundry?
One can hope, but the Foundry Dominion ships don't even include the Dominion Battlecruiser.
This is probably just an oversight, and adding the updated models might spur some movement on this. It's possible that the new Dreadnought has too much detail for an NPC enemy, but I hope not, as it looks pretty awesome.