It seems that the OP is asking for a system of "Hard Counters" rather than "Soft Counters," however due to the nature of the game a system of soft counters is almost a requirement. The main feature of the game is that although there is a fine variety of parts they can be arranged in an infinite variety of ways. Not only is there no hard distinction between a small ship and a big ship, that is kinda the point of the whole game. So gameplay that requires a hard distinction is generally a bad idea for Starbase. Though you can still have a lot of that "rock, paper, scissors" kind of thinking with soft counters; it just means that while Bomber usually beats Battleship, not always. A capital ship that has more laser turrets and fewer plasma throwers would be more likely to survive a bomber attack but less likely to win a match with another capital ship. Having different varieties of armor could have a similar affect.
Generally I don't like damage type systems, it often results in some very obvious choices. "These enemies are acid types, better equip anti-acid!" Though it could be better if damage types correspond to how weapons are used. Choosing the right armor type could complement your ability to avoid certain kinds of attacks. Autocannons represent a continuous stream of projectiles but so does the lasercannon. If they existed in the real world there would be major differences but in the game they are pretty similar, at least for the person being shot at. Thus the armor that counters one should counter the other. Meanwhile torpedoes function very differently, they deliver all of their damage at once and avoiding them is different. An armor that absorbs a certain number of hits regardless of damage would counter slow firing weapons, an armor that simply has X hitpoints would counter fast firing weapons. If 'reactive armor' existed in the game it would be the former.
I fully agree that we will need larger versions of various components. I don't think it is important in the short term, but as players start building bigger ships there should be larger components available. You can end up with some weird balance issues when you have massive capital ships that use fighter sized guns and engines. Movement thrust and firepower shouldn't be limited by surface area. There are similar games where late game ships are not only nearly invulnerable to early game ships but nearly invulnerable to each-other, such that it takes 15 minutes of constant firing to breach the enemy's armor. The reason is that their firepower is much more limited than their protection. You can't stack 15 turrets ontop of each other, but you can stack 15 armor blocks. I don't think that is likely in Starbase, if anything Starbase has the opposite problem, but still something to be wary of.