I think you are miss reading things..

early game, all the weapons you can add are only 1 damage. the 7 and 6, are either the cost, aka the build time, Or the amount of space it takes up.

as you research techs, each level, lowers the space it takes up, and perhaps changes build time a little.  So lasers 1-5, are exactly the same damage, only you can fit more of the 5's, than the 1's  (they also can look different)

then when you jump from levels,  like say going from missile to proton, or engines, like ion to impulse, things typically go up 1 number, the mass can change, but each sub level of tech, drops the mass a little

You also can use miniaturization, which lets you fit more things on the ship.

So if you take that phoenix M7, and click (upgrade)  and have researched enough techs, you could add lots of fire power, faster engines, longer range on life support, or even greater sensor range.   since i started skipping defense on small and tiny ships, they work better.

Also, building custom ships, you can basically piece things together to make 1000's of cool ships, and your tech research and opponents dictate your load out..   there are 3 types of attacks, and 3 types of defense.  Mix and match ships.. If your opponent has Missles and armor,  you can mount of ECM and Lasers. 

You can also use a thing called Upgrade..  say you make scouts, and then research survey module, you can then design a new ship, with the new module, save it as a different name.. aka   Ship 1A,  ship 1B,  ect..  then click upgrade, you can upgrade one or all to the new design for a bit of cash.   (i did get some weird bug with ships in fleets, that i could not remake the fleet. So i always un-bind them before i upgrade.. kinda a pain, but better than a bug)

anyways, making ships is always better, if the ship is listed, you should have all the parts to copy that design, if you didn't that ship would not be an option to build.