Thematically? Because the standard hardpoints are for energy turrets; they've been modified to accept munitions launchers, and associated ammunition magazines.
You could say the same thing about every Turret and Cannon upgrade in the rest of the game.
Y-Wings don't come with Twin Laser Turrets, they come with Ion Cannon Turrets. TIE Defenders don't come with Heavy Laser Cannons, they come with Ion Cannons. But none of those upgrades are modifications. All of them go in the space they go in.
I don't see any good reason why the Tubes couldn't have been a Hardpoint upgrade.
In addition, doing it that way would allow for my accurate pricing. As it stands, replacing only one hardpoint with a warhead or replacing 3, costs you 5 points regardless. Which, frankly, doesn't make sense. The cost should be based on how many of the things you're actually using.
Even within the upgrade slots, one could argue there's a big difference between swapping one turret for another and having to rip the power feeds out and install munitions conveyors. Heck, you probably ripped out the !capacitors and put in magazine bunkers in their place, right? ![]()
(I'm not hostile to the idea, and 'missile launcher on a capital ship' would have been just as thematically justifiable too. I'm just giving a suggestion for why it thematically could be what it is.)
Of course, really it's Balance Patch #3: This One Makes Your Hardpoints Energy-Free, so it's in the same slot as #1: Have Spare Re-enforce Actions and #2: Have Two Free Energy simply so you can't combo them.
Balance-wise, I don't disagree on the cost point. The 5-pt tax means that you either fly a loaded-to-the-gills missile boat, or you... don't. I guess this might actually be intentional; it means you're either a standard vessel or you're a missile one, rather than a standard-one-that-grabbed-a-spare-ion-pulse-missile.
That said, the latter would have made missile-fitted Gozantis attractive; as-is you're much better off taking a normal hardpoint (including that lovely turret of theirs) and Optimised Generators to keep the power flowing to it.
But heck, it won't be the last time a balance patch came in a model pack that was a terrible fit for it, right? ![]()

