Great that you got your little one in on the game. My middle daughter was all into games until she turned 12. Now, it's my 3 year old boy. He helps move ships, and completely enjoys moving the asteroids. True random movement!
For smaller missles, a la rocket size, I generally use the standard battery design rules. For larger ordinance, such as torpedo to ICBM size, I use seekers.
It depends a lot on your given background or flavor of the universe in which you're playing. For example, some Anime missiles fire in big packs much like a flight of seekers, but they're susceptible to intercept fire from point defense systems. In other Anime shows, those very same missiles are simply too smart/small/agile to be shot down. Thus, in Starmada, you could model them effectively either way.
I think, in many ways, we often tend to design weapons and/or ships to power game in the larger metagame, and forget the joys that come from using a set of limitations by common agreement to model a particular universe or story. This is especially true when designing ships/weapons for open gaming or ships to go against official published designs.
Conversions from one system to another are particularly prone to this. We tend to design the LARGEST ships to fit our perceptions and desired weapons load out instead of finding the smallest and most efficient design that captures the flavor of the original design or miniature used. This represents more of a focus on cause instead of effect. The ORAT, DRAT, and CRAT all help address balance, but sometimes it seems like a ship with a 200 rating is measureabley more effective than two ships of 100 each.
One of the cool ways that I've seen to address this type of thing during an open design campaign is to use resource points of some sort, keep track of different marks of ships, and design and deploy upgraded/updated/refitted ships so that the players can respond to each other's different strategies, just like historically happens!
Incidently, I agree on the H&C flavor text. I have just assumed that each fleet has a 'subsystem name' for any given type of beam weapon, much like we do in modern weaponry by assigning a system name. Sidewinder, sparrow, RAM, TOW, Patriot and Javelin are all modern missile examples.
