IIRC, small systems can't be hit, i.e. they don't contribute to hits-to-kill. My recollection is that the exploit actually goes the other way - you can ensure an "emergency reserve" of fuel that can't be destroyed by putting at least one small tank on a ship.
I agree with Father Tim here, this seems a bit "game-y".
This will also help alleviate some of the issues revolving around mounting fighter weapons on ships. If they get scraped easily, it removes an additional advantage.
If it wouldn't be a coding nightmare, I'd be be tempted to put small weapons outside of ship armor. If you want them under the armor then make them take up a minimum of 1 HS (and 1 HTK).
I'd apply this to other items as well. In the example above, the light small craft quality take would have a chance of rupturing if the cruiser too a sufficiently good hit (even if the tank itself wasn't directly touched). You could armor the tank but that would increase it's bulk and cost.
That way, small weapons/items are either cheap and easy to toss onto a design or they are built to military specs and heavier and more expensive.
I don't know what this would do for your version of the LACs though (I haven't played with those yet).