So, I was flipping through my Rogue Trader core book, getting some ideas for ships, and noticed that it described the cruisers as carrying a fearsome payload of weapons, from lances and macrocannons to missile tubes, and then it said most rogue trader ships take out the missile tubes for increased storage space. After reading that, I also noticed that this seemed like a convenient excuse taken to not have to write up stuff for missiles in the book.

Now, I understand that the purpose of many Rogue Traders is to make money and garner fame, and if they can put on a veneer of furthering the bounds of the Imperium and its beliefs over their stealing, xenos-consorting, and anything else they do, all the better, but what says that my "command" ship, where I and my fellow Explorers act from can't be kitted out to fight and carry freight/booty, while being escorted by another ship or two designed to be escort/protection vessels, to defend my plunder till I get home? These ships could easily be bigger ships, too, if we had the Profit Factor, and thus might still sport their ordnance. Are there rules and details for missiles and torpedoes the bigger ships might carry?

Don't worry. They have rules for it in Battlefleet Koronus. They just didn't get them in the book in time for the Core.

Isn't there a Missile Battery in the core book that just nobody uses because it can only fire every other round?

Umbranus said:

Into the Storm: Jovian Pattern Missile Battery. Fires once every other round.

Also, what you're looking for are torpedo's, quite different from missiles because they're effin huge and expensive.