I have more problems with missiles than just the thruster unit. The missile example that started the discussion is as follows.
The current "standard" missile design, per Errata 07, is, "a 5G6 continuous burn (36 kg, Cr3,600, TL 8), mass sensing (1 kg, Cr1,000, TL 10), proximity detonator (1 kg, Cr500, TL 6), high explosive (10 kg, Cr500, TL 6) warhead missile (all produced at their standard tech level), costing Cr5,600 and massing 48 kg. This price does not take into account tech level effects. At TL 9, this missile costs Cr5,540; at TL 12, it costs Cr4,480."
I will not get into a discussion of at 1 kilogram mass sensor being able to distinguish between the adjacent mass of the firing ship verses the very distant mass of the target.
The warhead is TL 6, along with a TL 6 proximity fuze. Presumably, that means the missile cannot be relied on for a direct hit. The warhead has to be fragmentation, as blast is a meaningless concept in a vacuum. A High Explosive Plastic/Squash Head warhead is ruled out by the need for a nose sensor.
In Supplement 7, Traders and Gunboats, there is a good description of the amount of damage interior partitions and bulkheads on a commercial ship will take. To put a man-size, say one meter diameter, hole in an interior partition requires 100 damage points from an energy weapon, 100 damage points from an explosive charge, or 1000 damage points from a projectile weapon. For a man-size hole in a bulkhead, 1000 damage points from either an energy weapon or explosive charge are required, with projectile weapons being useless. Deck floors are treated as bulkheads.
In the Double Adventure 5, Chamax Plague and Horde, 100 points of acid damage will breach an interior partition, 1000 points of damage a bulkhead. However, the Chamax also, using acid, burn one meter holes in the hull of the Shaarin Challenger and the derelict pinnace. Given that, it would appear that the strength of the hull plating is very similar to that of the bulkheads.
Now, when I think of small arms for penetrating any type of ballistic plating, I think serious small arms, like a .30-06 firing AP ammo at close range. My penetration charts indicate that to order to have only a 5% change of penetration by that round at normal impact and close range, you need either 1.1 inch of mild steel plate weighing 43.1 pounds per square foot, or 0.75 inches of special treated (i.e. ballistic) steel at 30 pounds per square foot. That means that your bulkheads and hulls are thicker and stronger than that, and your interior partitions are pretty thick too (read not light weight as one would think).
A 10 kilogram fragmentation warhead is not even going to dent that thick a hull, so drop the proximity fuze, nor is it going to punch a hole in by simply detonating. Now, a direct hitting High Explosive Plastic/Squash Head round of roughly 4 to 6 inch diameter will blast a 6 to 8 inch diameter disc out of that thick a hull and project it into whatever compartment is impacted. A space ship is not a very congested and small volume as a tank, so your chances of crippling damage are very small.
If you really want serious missiles in the game, then start talking ones that weight in the hundreds to thousands of kilograms, and cost serious money, like 500K Credits on up.