It's not anti-subsystem missile for unexpected issues so I mostly use it according to it's purpose assigned by V.
Whatever V makes the Trebuchet to be in their descriptions, realms of gameplay tend to disagree. Both the Treb and Maxim fill a very specific role that is met pretty often during the game, and it's a real waste to use the ammunition to shoot down secondary targets that could be dispatched just as easily with dogfighting weapons or by your wingmen. Two Trebs can take down a single bomber, or efficiently get rid of a corvette's worth of beam cannons or even defang a Ravana with some luck. What's worth more?
Of course, there are instances where the relative value of multiple beam cannons is lower than a couple bombers, but that's usually due to the ship with these beam cannons being massively displaced in the battlezone.
IMO these arguments are rather self-evident after several years of playing Freespace?
The mission designer isn't supposed to expect the player to read his mind, of course. However, I believe that the mission designer should be at least allowed, if not also encouraged, to create scenarios that reward and/or require the player to employ certain ways of thinking about possible future developements in the battlezone. This also works very well when combined with immersiveness. Look at this like: you're military. The responsibility of the military is to be always prepared for whatever comes and threatens you. You're fighting Shivans of all things. With such an enemy, you must always expect the worst. This means you need to manage your resources carefully to minimise the chance of being caught with your pants down.
This is exactly why after a fight you should always rearm and let all your ship's energy reserves recharge. Or why you take a bank of Trebuchet or Maxim with you for an escort mission, if possible - even if it isn't said that there will be a capship to defang around the place, you have to be prepared for one. Or why warships join formations - to be more resilient in case of fighters and bombers, and to be able to more efficiently respond to threats.
For me, it's a large part of the immersiveness of a mission. Treating the player as if he's thinking like the pilot he is - fighting against an extremely dangerous foe, expecting and preparing for danger and always trying to make the best out the current situation, as compared to a person who sits there and thinks "well I'll just follow the common mission design tropes, what can go wrong?".
I just think, Nyx
That you've been simply caught with your pants down thanks to you following one of the popular escort mission cliches and there's nothing in your defense for that
That's why I think this mission is better than the average, at least in this respect - IIRC you're being informed during the briefing that there are enemy capships around the place and you're getting a slight slap for assuming the size of the force or following the common mission design trope.
Ultimately, it's nothing tragic - the worst that happens is you lose several minutes of gameplay and give yourself a slight mental facepalm and then replay it and win the battle. And if you manage to be prepared, you can give yourself a mental self-high-five and then feel like a pro