Well.... Aurora IS a role-playing game. The Author of the game Steve have explicitly stayed away from detailing things like government, politics and cultural mechanics for this very purpose and it IS up to the player to decide if a specific style is optimised based on the cultural and ethical rules of the society it is built in.
We have to imagine that ships are not built in a vacuum in any game and people who role-play often either decide on a specific way they like to do things or do things as things happen in the game and base every decision made based on the information given within the game. Using your own knowledge of game mechanic and such is pretty much forbidden in such scenarios.
Many people do a variation of these types of role-play.
This also mean that a Star-Trek type of ship can make very much sense and be quite effective from that point of view, it does have to be pretty big and expensive though.
There is nothing wrong with just playing the game mechanics and that is your choice... but optimisation always comes down to the personal rules of the game from the person playing the game. The game is built around that fact, it is simply a tool set with mechanics for players to mold to their harts content.
If someone send an entire fleet with their survey ships in order to scout and keep them safe you can't say that is not "optimized" play because loosing a small survey vessel once in a while is far less resources than protecting them with an entire flee all the time. This depend on the political climate in which why this decision was made and how much you value skilled labour and the lives of your crew, officers and scentists.
Aurora is NOT a traditiona game in the sense there are no victory conditions or even any way to "WIN" the game. You can keep playing until your computer burns the processor for having too many systems, NPRs and civilians in play...
You're talking about multi-function ships in a fleet context. (And I strongly disagree on that, but that's beside the point.)
But for an independent cruiser this isn't relevant. You aren't choosing between 20 beams on 10 ships or 25 beams on 5 ships, you're choosing between 0 beams or 2 beams or 5 beams. Of course, it's not beams that are really the sticky point there. 2 beams out of a possible 5 may lose a fight, but it's still reasonably functional. 2 ASM launchers out of a possible 5, though, very likely doesn't do anything but entertain the enemy's missile defense suite. Missile attacks on anything but defenseless targets are a go big or go home situation.
I agree... using missile launchers on an independent cruiser make very little sense as you need weight of fire. In that case you would need use box launched missiles as they will not be expected to be close to a resupply point anyway. But beam would be my preference as they are more useful overall for self defence. Missile weapons are usually more of a group effort to make them work properly.
When talking about missiles I rarely find that allowing ships to fire ASM at all make much sense until you have very strong cloaking abilities. Fighters and FAC do this so much more efficiently. They are quicker to both build, upgrade and specialise than any ship can ever hope to be. They are faster, stealthier and just deadlier in so many ways. Fighters are so much easier to build early in C# that the time for missile cruisers pas so quick I rarely see them at all even in my campaigns of 10-15% science rates.
I only ever use ASM missile for system patrol craft, fighters and FAC these days, this has mainly to do with role-play because it sort of falls naturally from how things turns out. Putting full size launchers on huge ships simply limits the volume of fire and using box launchers on huge ships is extremely limiting on the type of missile you can use and reloading of the platform is tricky when far from home and they loose the very important stealth factor (before cloaking that is). On any ASM ship just rip out the launcher and part of the magazines, plug in some hangars and some extra fuel and off you go...
The only ASM and use of regular launchers is for engaging opposing small crafts, so size 3-4 missiles with say 4-9 yields typically. As these smaller ships have much more limited defence capabilities using such system is highly efficient. Against dedicated PD defences then regular sized launchers are almost useless unless you are seriously outmatching en enemy.
I use specialised ships too but mostly in rather small numbers. For example Monitor ships... usually a ship at 10-20kt range with the most powerful engines I can build for speed and extremely short range, usually around a billion or two kilometres. These will have to be moved by fleet tugs to do anything useful outside guarding colonies, jump points or whatever real estate they are built to protect.
Specialisation is more about how much variation I can put into a ship within the 20% difference that a single yard to do with any ship type.
I'm likely to have like one frigate type, one destroyer type one cruiser type and one carrier type ship and then have allot of different variant of them that reside within that 20% variation.
When it comes to anti-missile defences then due to the nature of missiles I'm never ever going to deploy a fleet without anti-missile defences so there is NO loss to put some PD on every capital ship.
The Frigate usually is an older ship that used to be a destroyer, perhaps changed a bit but slower (perhaps old engines) and their primary mission is patrol, scouting and performing escort for my supply train or other high value commercial designs or perhaps a squadron of Monitors. The Frigates are not suppose to operate far from supplies and fuel.
I then have the destroyer who in general is the main escort and patrol ship and its primary mission are anti-missile and will primarily have most of those systems. The rate at which I build destroyer would the correlate to how important I think this mission is to the overall performance of the fleet.
The cruiser if the fleet flagship and the one with the best sensors and usually a bigger hangar for more dedicated scout crafts. They are sort of an overgrown destroyer with more space dedicated for scouting and perceiving the surroundings better, it will have the strongest armour and shields and a really powerful beam complement.
The carrier is more like a mesh of a typical battleship and carrier... usually about 25% hangars and the rest is armour, shield and beam weapons and a good chunk of PD weapons too.
As almost all of my ships use hangars there is an option at times to fill most if not all of it with strike crafts. This has happened when there has been a need for a dedicated and very strong alpha strike at a specific target. It is good to have options that way. Otherwise scouting is the primary function and anti-craft operations a secondary role.
Fighters is usually a weapon that I see as the main branch for deep space combat. If I'm to attack an enemy colony or JP I'm more about brute force using the defensive nature of my much stronger fleet to throw any defensive missile barrages to the sides and engaging them at close range with both missiles and beams until I win.
Obviously this s not one correct way to look at the game... this is just one natural way that it seem to develop for me in most games.
Building ships this way you need to build allot less shipyards... ships are easier to upgrade as they come in smaller sizes. Yards are much quicker to retool as a direct effect of that reducing the time in which you can upgrade existing ships. You can very easy change a ship from one type of a class to the other as it is mostly switching out components for other components, so very little material costs, just a small amount of time. You yards will also tend to be in use allot more as each yard service so many more ships of a single class. Adding slipways are more industry effective than building new yards.
Ships also by definition work very well both alone or in small groups.