Generally speaking, if you're jumping with rounds on the rails, something has gone horribly wrong and you're probably going to die. This isn't a really USEFUL arrangement, it's an AMBUSH arrangement-you jump in, deck crew unships the missile cans onto the rails, wait for someone to get greedy/frisky/spot you, and engage them...or sneak up and engage them because they're not expecting you to show up with THAT kind of firepower.
As for dropships, I reckon that Phil Cartwright probably would've chosen something like a Furey or buccaneer (more likely a Bucc, since those aren't exactly famed for their space engagements and they ARE on the loose open market as civilian vessels, unlike Leopards that are dedicated military transports).
For monbvol's modified Merchant
above, it looks like the missiles would have to be stored in the attached Dropships, and transferred out after arrival. The
Buccaneer as you mentioned would be a good design, as it is a very good cargo carrier. The 303 tons of cargo for the modified Merchant would only allow up to 6 Killer Whale missiles, and that is only if you use all but 3 tons of cargo.
I see a mission going something like this:
1) The Buccaneers would attach to the Merchant
2) The Merchant would jump
3) The Buccaneers would toss out a few missiles to float in space
4a) The Buccaneers would head in-system as honest traders
4b) The Merchant's crew would attach the missiles to the launch rails, and either wait for pirates to approach or try to creep in close to a pirate
The main problem I can see is that you are putting your very vulnerable Jumpship potentially into weapons range of a pirate vessel. There will be nuclear warheads in the Killer Whales, but the Merchant is still an egg shell that can be cracked by a Medium Laser everywhere except the Fore Sides. The Merchant has to strike first, and the Captain has to be certain of the target once you start tossing nuclear warheads near rare/valuable Jumpships.
Combat Dropships might not be as strategically flexible as a Jumpship, but they are far more expendable and capable. In this case I'd be tempted to use the Buccaneers to drop off Killer Whale-T missiles while closing, then tell a pirate to either surrender or the ship far outside their weapons range will activate the missiles. If the pirates try to fight the Buccaneer's crew (either with their Dropship's weapons or their personal weapons once the Marines on board), they will get nuked.