A ship that is all weapons wouldn't just be worse in other areas, it would be worse in the one area it's specialized in (assuming your goal is to fight and kill, not to just have weapons). There's synergy between different systems, an effective warship needs armour, sensors, fire control, C&C, ECM, ECCM, the ability to deploy and maneuver, damage control, redundancy, damage absorption, enough power to fire all those weapons, the ability to sink heat from all those weapons, ammunition, maintenance, point defense, staying power, a reasonable price and a suite of offensive weapons. You're making a lot of sacrifices when you give up several of these for the sake of more weapons.
And I think I just explained why a comprehensive point buy system would be maddening, while I was at it. Instead of trying to figure out the perfect balance, we should look at what we already accept are plausible ships, the ones that we've accepted as part of the genre all along.
If people want to make a slow ship with lots of weapons, yes, we can let them. We don't have to reward or punish them with a point-buy system, though, we can instead just assume that all else being equal, a system defense vessel or monitor will be more potent than a fast attack craft if they, for some reason, duel it out in a slug-match. In practice, ships are designed for a purpose and ships that aren't used the way they're meant to be used should be at a disadvantage. There's many factors to consider.
It's the solution, not the problem, if we make it clear what ships are meant for and how well-designed they are when they're approved and then use our judgement on how they interact, later. If we don't agree, if one person thinks a design should work great and another thinks it's absurd, then the issue is that we never agreed on it, not that we didn't come up with strict rules.