It’s been pushed that fix mounts don’t require tonnage or power what been ignored is that they do require a Hardpoint, you just can’t bolt them just anywhere at the minimum they need control runs and they still require a gunner. So for example that Freetrader or Fartrader which already has 2 turrets has to rip one or both out to place that fix mount and you can’t actually just add that ton back as cargo (it’s where the turret was) tho I suppose you could use it for missile storage. But ignoring all that your biggest issue is going to be your sensors, civilian or basic sensors are unlikely to see that pirate at a range to make your missiles effective (especially since at TL 12 beam Lasers can have long range). Another problem with a fixed mount is the missile detecting the target, does the missile take sensor input from the ship in which case you have the issue with the ships sensors or does the missile use it’s own sensor input which case you have a firing arc.
I am not sure anyone has been ignoring the hardpoint requirement for fixed mounts, but as we were talking about 200 DTon hulls having one or two isn't an issue. The cases where people were talking exotica regarding firing aerospace defence weaponry out of cargo airlocks and using docking clamps for auxiliary vehicles do not require ship hardpoints since they are mounted or their ground weapon carriage or on the auxiliary vehicle respectively.
There is nothing in the MGT2 rules stating that tonnage released from removing a turret cannot be re-used for a different component (including cargo). Check the refitting rules in High Guard. You are making assumptions about where turret space is allocated that are not supported by the rules.
The concerns you state about sensors are valid, but they apply equally to any other sort of weapon. Missile fire is no more dependent on the the firing ships sensors than any other weapon. Sensor lock gives +2 to all attacks (and only Gunner skill and range modifiers are ignored for missiles). As for range, having a longer ranged weapon doesn't mean you cannot fire it at shorter range. Unless you are firing at close enough range to lose the smart trait, missiles fired at less than maximum range become more effective as they get to the target in less turns and therefore provide less opportunities for EW. Your sensors are less of an issue than the quality of the targets sensors as EW can rapidly negate your entire salvo.
All weapons "require a gunner"**, so this concern is not limited to missiles but only missiles do not suffer a penalty for an unskilled operator. You may have decided that weapons can only be fired by dedicated gunners in dedicated gunner stations, but the rules don't say that. Firing ship weapons uses the Gunner skill (p116 core rulebook) - though this is a bit sloppy since missiles don't, but in the same way that unskilled people can fire hand weapons without the relevant skill at a -3 penalty I see nothing specific that requires you to have at least level 0 in Gunner (Other than to reload sand casters and missiles). So a gunner is just someone who conducts gunnery. The pilot can fire any single turret at -2 but the wording indicates that they don't suffer any penalty for firing fixed weapons (plural) so you don't require a dedicated gunner and according to the wording the pilot can fire all fixed weapons (I would rule they would have to be linked for that and all at the same target). This is more common on fighter craft of course where there may only be a pilot. Obviously they would suffer a further -3 if they didn't have the Gunner skill.
That said if you have decided to arm a merchant (regardless of the weapons) having the Gunner skill (and another finger to press the trigger) makes more sense. Any of your other crew (particularly ex-navy) might have Gunner as a secondary skill and I assume bridge stations are multi-function so one of those could do it. If you have dedicated gunners they are the lowest paid crewmembers on the ship and I presume they would double up as unskilled deck hands when not in combat. You need to allocate accommodation and life support which further eats into your profits. Personally I would consider using droids as they can be very cheap (they don't even need to be mobile) and have no life support or accommodation requirement. Whilst the capital outlay is higher it is quickly rendered trivial compared to recurrent and opportunity costs**.
As to firing arcs, I don't think these are a thing. Any thrust not allocated to movement can be allocated to Combat Manoeuvring. In this the captain orients the ship to give his gunners a more stable platform "along the optimum attack vector". For an aft mounted missile mount during a stern chase, you are already pointing at the enemy. Unless you can break sensor lock and "go dark" there is usually no benefit to moving other than directly away from them since there won't be any cover nearby. In marginal cases you might need to choose between directly away from them vs towards the jump limit or the port, but no sensible pirate is going to attack when you are a few minutes from one of those safe havens given the journey is usually multiple hours, logically you would be hours away.
EDIT:
* P164 states that each turret requires its own gunner and each bay requires its own bay weapon gunner. There is no mention of fixed weapons requiring a gunner there. Similarly there is no Gunner(Fixed Weapons) specialism. P183 however states each turret or fixed mount requires just one gunner. I tend to assume that fixed weapons are a subset of turret weapons (as they are often bundled together) but arguably they should be their own specialism or even unable to have a specialism.
**Actually since you only need a homing primitive brain with Gunner(specialism) 1 and it need never leave the ship, you could build a really flimsy walker droid for a few KCr that could operate a normal gunner station. This would be cheaper than a real gunner after less than a month. An actual sophont would need to designate the target, but this could be vocal and needn't be anyone with any particular skill (though you would like to hope it would be locked to competent crew). It could also be assumed that it any sensor locked vessels were automatically designated.
From a game perspective this could be a good choice as you don't require a player to be a dedicated gunner (which could be dull for most of the time) or allocate to a skill they may never use. The referee doesn't have to run a load of NPC's and then have to work out what they do when the rest of the team go planet side. It doesn't remove agency form the players. Instead, gunner droid unfolds from its cupboard when the red button is hit. It does exactly (and with INT 1 I mean EXACTLY) what it is told to do by a player character for precisely as long as necessary and then after the fight folds itself back into its cupboard. Since it has one ability players won't be tempted to start taking it round town with them for extra firepower or utility (other than comedy value) since it is absolutely appalling at any other task.
Is there nothing droids can't do
