Strictly my own opinion, but I think since they had the Millenium Falcon title card, they needed to add the Slave 1 title card. They give the MF title card the Evade action. I can see that, as the Falcon was modified to be more elusive to attacks. What to do with the Slave 1 title card? The game designers see the Firespray as a weapons boat, tricking it out with HLC, mines, missiles. Hey, why not give it proton torpedoes as well? And I'm sure SOMEWHERE in the canon that the Slave 1 uses PT's, and they didn't want the fanboys saying,"The Slave 1 clearly uses proton Torpedoes in the 3rd cel on page 28 in this comic book, so why didn't you give it the Proton Torpedo slot?" I give credit to the FFG researchers for finding that somewhere and ioncorporating it into the game.
I would agree that I don't necessarily think it's the best option for a secondary weapon, but the game designers just gave us another option, and options are good. I'm sure you'll see someone at a tourney run the Slave with PT's, if for no other reason than they can.
And two things to keep in mind, all of these secondary weapons that you trick the Slave out with can only be used in the front firing arc. No 360 degrees for the Ion Cannon. The real trick is maneuvering the Firespray in order to use the secondary weapons, especially missiles/PT's, because you need a Target Lock to do so, which means you need an action, and there are currently many ways of keeping the Firespray from taking its action during the Perform Action step (collisions, asteroids, red maneuvers). Like others have said, Squad leader will help mitigate this. One of the reasons the HLC's work best is that you don't need an action to use them, unlike Missiles and torps (Target Lock), or Proximity Mines.
So, in order to use the PT's, you have to do all of these things:
1. Avoid collisions (unless you're getting an action from Squad Leader)
2. Avoid asteroids, both in moving through them and landing on them.
3. Not have a stress token
4. Use your action for Target Lock
5. Have the Target locked ship in your front firing arc
6. Have said ship at range 2-3.
7. Then you can use your Proton Torpedo. Which, since you've spent your Target Lock, you don't get to reroll any of your dice, unless you're Krassis, in which case you get to reroll 1.
8. Then the defender gets to defend.
And given all of this, I think Shadowjak's tables have shown that the expected number of hits for a proton torpedo is less than 2, so you're on average not going to kill anything anyway.
And if you want to make the case for obtaining a Target lock in a previous turn and using a Focus, you have to go through this list again in order to do so. It's a lot of hoops to jump through for a 1-trick pony that has little chance for actual damage.
This is why most people say the Heavy Laser Cannon is better. The Range is the same, the number of dice is the same, the firing arc is the same. The differences are that you don't need an action to use the HLC (big, big difference), you won't get a crit with the HLC (unless you have a mercenary copilot, and the general consensus is that crits aren't that much of a difference in the grand scheme of things), you can reroll your dice with the HLC if you do have a Target Lock (which is necessary for the PT as well), and you can use the HLC mulitple times (another big, big difference). The HLC is 7 points vs 4 for the PT. That's a small investment for a big difference in usage.