I voted no for these reasons:
1. I think it would still be interesting to continue using effect and slave systems to modify weapon behavior. Otherwise the missile weapon system will be its own system type, and balancing and improvements to the main weapon systems (beams, cannons, pulses) will not translate to missiles, inevitably requiring extra effort by the devs.
2. I would like to see the missile "style" effected by the missile effect.
Examples: High-speed Dumb-fire: Missile turns into a plasma blast. Low-power missiles should continue to be a beacon, with a simple 1x1x1 hitbox. That makes smaller, multiple-missile launchers more viable to fly through point-defenses. (Warning: encourages missile shotguns! Not so good!) Normal (high-damage) and homing missiles should gain a regular missile model (client configurable?) that has the regular 5x5x5 hitbox.
Other thoughts:
On the subject of a missile model: I don't think it should be a model in the conventional sense. I think it should be a saved block template, so people can "build" their own missile models from all the blocks available in-game. Since the hitbox would not change, the model could be anything and any size, and the mechanics will remain the same. It would act bizarre for large missile "models", but then you could have a more detailed model, even if it looks like it should be more easily shoot-able than it really is.
Actually, now that I mention it, I think most in-game models should be scaled-down saved block templates. Inspired by someone's block-made rifle in a screenshot, I think it would be a great way to add great user-generated content to the game. By integrating scaling, you could build the rifle (or whatever model) as a ship with full blocks, then save it with an option for "automatic normalization", which takes the ship model (in this case, a giant rifle) and automatically "normalizes" it so that it fits down within a 1x1x1 block size. Helmets, armor, shards, chairs, desklamps, stairs, anything could be built with this system, and effectively wouldn't add anything but a relatively small ship template and associated scaling level to the game. I think that would be a huge way to save space while getting good detail on new content.
With that idea of normalization, maybe missile block templates could be "scaled" down to the appropriate hitbox size, so that a 30x30x10 missile "ship" would scale down to fit in the 1x1x1 size to fit the hitbox in the case of a low-power missile, or down into a 5x5x5 size to fit the hitbox in the case of more powerful missiles.
