I don't know how the Standoff and UE guys will do it, but I think my take is that they are seperate. The torpedo room fires torpedoes, and there would some type of seperate launcher that fires the cruise missiles (which are in effect, planetary bombardment CapShip missiles).
I actually thought about this a lot when i was making up technical specifications for my upcoming webpage, how many missiles/torpedoes a destroyer could/should carry. I had to do a couple of considerations first.
1) The number of torpedoes available to Confed forces were low, as said in the WC2 manual. If I remembered End Run correctly, the Tarawa used up her entire supply of ship-killer torpedoes in just two or three strikes. It would be really really . . . dumb if our Broadsword and Longbow squadrons didn't have enough torpedoes because most of the torpedoes we manufactured all went towards our destroyers and cruisers. Especially destroyers, because Confed has a *lot* of them. They are basically cheap mass produced warships.
"Pilot: Hey Colonel dude, our Broadswords need more torpedoes man.
Colonel dude: Sorry Lieutenant dude, our carrier's running low on torpedoes. They didn't send us enough for our carrier.
Pilot: But Colonel dude! We got four destroyers and two cruisers in our battlegroup, and each one has over two dozen torpedoes! We can just use them!
Colonel dude: Of course my hairy-assed child, but because BuWeaps said the number of torpedoes are low, we have to keep them low. That's how the Confederation works. So sorry Lieutenant dude, you'll just have to take on that fleet carrier with just a single torpedo on your Broadsword. And did I mention your wingman won't have any?"
2) I also had to find a way to keep things balanced. If destroyers had a lot more armor, shielding, and staying power then a bomber, and could go almost as fast (Gilgamesh's 250kps compared to Broadsword's 320 kps), and give a much much much better ship-killing capacity then either Broadswords or Longbows, then they would effectively render bombers obsolete and we wouldn't have needed them ever. So I had to find some way to give a good justification why the Confed military uses torpedo bombers instead of capital ships like destroyers for primary anti-ship roles. This is true in case of the Broadsword, which has no afterburner and isn't that much faster then a destroyer. So I had to put some sort of limiting factor on the destroyer's anti-capship roles.
3) I did up my checking on WW2 destroyers and even our destroyers of today. If I remembered correctly, WW2 US destroyers had 10 to 12 tubes (so they can fire that much in one salvo), but very very little reloads. Some had no reloads at all, and others only had up to four. And I looked up today's specs as well. Our modern day destroyers and cruisers tend to carry just 8 anti-ship missiles. Of course, I don't want to base everything WC on our military of today, but I took that balance into account.
4) I think WC has made it quite clear to all of us that when it comes down to it, the main striking power of Kilrathi or Confederation navies come from fleet carriers, with torpedo bomber squadrons. It's that "reach out and touch someone" capability which explains why Confed/Kilrathi/others primarily use torpedo bombers to attack capships. If the Confed fleet lost their entire carrier force, then they are screwed. All the destroyers with all the torpedoes in the Confed inventory wouldn't do a thing to turn the tide of the war in their favor at that point (if it ever happens). If a destroyer's ship-killing capacity was that good, then Confed can just say "oops, we just lost our carriers. But we got badass ship-killing destroyers, we can still win the war!"
5) I personally think twelve torpedo tubes with little (around 4) to no reloads is a lot better then four torpedo tubes with 12-16 total torps (4 in tubes, 8-12 reload rounds). More flexibility, less logistical time and manpower required (destroyers are small vessels), and more useful in emergency situations where one has to attack a Kilrathi supercarrier