Fridge Brilliance - "Trust in the rust" meaning the older the ship, the more likely it has survived many battles.
It's also a play on "In Rust We Trust" a common saying among Minmatar pilots.
Fridge Brilliance: The Jovian backs down when John gets really angry in Clear Skies 3. This makes sense in the context of Jovians having bred/engineered anger out of their society. A Jovian from the Technology Gifting Department may not have the training necessary to effectively handle human aggression, and so gives in when John's compliance isn't immediate and automatic.
Fridge Logic: A very serious one. Ghost has the capacity to disguise an assistant as Mr. Smith convincingly enough to hold a short, terse conversation with Rourke without raising any suspicion. He manages to convince them to take what he needs out into the middle of nowhere. So why does he blow up the ship? It seems like there'd be a very serious risk of his priceless artifact going up in smoke along with it. Needless to say that the destruction of said ship would also very likely give Rourke a very personal motivation to seek revenge which has been a demonstrably bad thing to do in the past. Why not simply continue impersonating Smith, have him drop the cargo, and then fly off? If they'd done that, Smith would very likely never have even known the power plant still existed until it was too late to do anything about it.
Ghost does prove to be a Blood Knight, however, and may just have not wanted his Stealth Bombers to go to waste.
Also, they had contacted the real Smith by that point, and thought something was up. Ghost may have guessed as much.
Fridge Logic: John's character model is Barney Calhoun, Civil Protection uniform and all. This makes the rescue scene in episode 2, in which JR and crew disguise themselves as officers wearing those same Civil Protection uniforms, kind of weird, as it makes you wonder both why JR is wearing such a uniform already, and why he had to "disguise" himself seeing as he's already wearing the uniform.