Ship design is about all about size-effective hulls.
Long ships and tall ships apparently got differences.
You should first start with really small ships to get the hang of it.
There's also two important things to think about: "Walkability" (is it possible to walk inside it when lagged?) and "Organization" (or whatever you like to call).
For example, in a combat/lag situation, you should be able to leave the ship via hull doors or teleports quickly, or even access the right places in lowest time possible (cargo hold/teleport room/bridge).
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My thoughts on ship-design
In summary, making a size-effective ship will result in a maxed out, overall good ship, in every TL you want.
Making a Huge ship really doesn't appeal to me, because this ship will need more gravity/wormhole/power plants, thus making the power requirements bigger, thus getting their power/shields/fuel/weapon systems drained out very quick, depending on the TL and Fuel Capacity/Power Plant Units.
I like to max out my ships as much as I can, but ship design is something really individual for each people, and that's why it's fun.
About the ship:
Of course you can make a huge ship to transport other starcrafts inside it, but that will need a huge vehicle bay and a lot of decks (if you gonna transport a 7-decker starship, your bay will need to be 8 decks tall).
With that huge bay, you will just be able to insert a bridge, officer/crew quarters, and a gravity well for transport between decks.
Am I forgetting something? Yeah, the engine room.
At least 600 units of powerplants/gravity drives and maybe ~200 wormhole drives. I think it's more, but 1.400 equipment modules is already TL7, and you still lack all the other equipment (shields, transport, sensor, quarters, consoles, turrets) that can sum up to 200 if you're minimalist....
That's a T8.
Remember: I think it needs WAY more than that in equipment, plus the Hit Points will be HUGE and rush through TL10 IMO, and I only thought about ONE 8-decker 15x15 bay. Which I still think is small.
Transporting huge ships isn't a good idea...
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PS: Don't forget you only start to really design ships on TL7, when you're able to build all equipment and rooms.
This makes you think in a lot more stuff.