So you’ve gone for a through deck design, that’s not a bad choice, but it’s not the only one.
In a modern Navy we see increasing use of through deck designs. It’s an efficient use of space and offers landing spots for VTOL craft. Conversely, the American super carriers have a slanted deck with a separate take off and landing area. This allows simultaneous take off and landing operations and is possible through the use of a catapult. Through deck designs (these days) don’t tend to have catapults and rely on STOVL designs and/or launch ramps – i.e. the fighter requires the length of the deck for the take off run. Which means that takeoff and landing operations cannot occur simultaneously.
But that is a water based Navy design. We’re talking futuristic space carriers and the laws of physics allow for different options.
There’s the B5 style Cobra Bay drop racks and the launch spindles of the Excalibur (which I quite like, but requires a massive ship). Or there’s the drop ramps we use in Atlantis DSV which are (I think) similar in concept to SAAB. Or there is, of course, the BSG style landing bay with separate launch catapults, a massive extension of the classic Navy carrier design. Then, of course, there is the classic hanger as used in SGA and Trek, with a large room with a single door that opens to space (and a separate maintenance facility – how else can they store so many shuttles on Voyager...). And who says fighters have to be stored internally, they could be docked on the outside (B5 again) except when maintenance is required.
So, a through deck. Not a bad choice but it does force the design somewhat. Your hull needs have a hollow tube large enough to fly a fighter through it. This allows for a “bolter” in the event of a failed landing attempt (i.e. the pilot adds power and aborts the landing), so the tube needs to be high enough to allow this, probably three or four decks worth depending on the size of the fighter. The next question is how many runways and in which direction. A runway is aligned fore-aft on a Navy carrier because of the need to get wind over the deck, the ships steams into the wind to maximise airflow across the aircraft wing during takeoff/landing. Obviously this isn’t a problem in space, but there are other considerations. Is your carrier going to be moving during launch/landing operations? If the ship itself is going into combat then the answer is probably yes – in which case landing from the side is probably not smart as the landing bay will be moving laterally relative to the pilot, which makes it harder to line up. If it’s fore-aft, relative lateral movement is minimised (assuming the carrier flies in a straight line) and the pilot just needs to make sure that they are flying faster than the carrier (assuming they’re landing from behind, taking off forwards). A fore-aft takeoff/landing makes for other complications, and that is clearance. The approach path needs to clear the nacelles and (preferably) any wake from the impulse drive.
The next question is about the fighters themselves. Are they VTOL capable? Do they need a full length “runway” or is it suitable to just have an open deck full of landing spots that they can hover over and land on. Are they going to accelerate inside the hanger or just coast until they are outside and then accelerate away. Also, what is the size of the air wing. The answers to these questions will alter the arrangement of the deck.
How many runways do you want? Do you want a single, central runway, or two (or more) parallel ones? On a fore-aft arrangement, the parallel ones could make it harder to clear the nacelles. Are the runways on the same deck – if the ship is big enough they could be stacked vertically. Will the runways share the same hanger space, or will they be segregated?
There is more to a carrier than just a floating runway. You need space to park fighters prior to launch, you need maintenance facilities and a means to get the fighter there, you need a dedicated command and control facility which means a decent sensor and comms array.
Parking first. It would be preferable to keep the runway clear at all times. Whilst it is possible to “store” craft on VTOL pads, it is good practice to clear the landing pads to reduce the likelihood of accidents snowballing. So dedicated aircraft stands should be beside the runways. These don’t need as much height clearance as the runway itself (assuming ground/hover taxiing is possible).
Next is maintenance. A secure and controlled area is required for maintenance of fighters, this area needs access to storage areas for large item spare parts (or possibly industrial replicators), plus the equipment needed to strip and rebuild the fighters. So gantries, cranes (antigravs) etc. A means of moving the fighter from the parking area to the maintenance area is also required. On a Navy carrier the maintenance area is on a separate deck, so a lift/elevator is needed to move the fighter down. This is not necessarily a must, they could be on the same deck. It comes down to do you want to increase the depth of the ship by a couple of decks (fighter plus clearance to work around it) or increase the width/length.
A final thought on the location of maintenance/parking/launch facilities is the amount of protection required. If there’s an accident in any one area you don’t want it to snowball into other areas. Fighters contain fuel and munitions and you don’t want a single fire to take out the whole carrier. So consider segregation, armour, positioning within the hull, vulnerability to external damage etc.
On to the support systems. The carrier will need a dedicated command and control facility for the fighters, somehow the takeoff/landing operation needs to be controlled and monitored. Ditto for flight deck movement. This means high resolution close range sensors and communications. Then there’s long range sensors, the more warning the carrier has of a threat the better chance it has of scrambling its fighters before entering combat range. Once the fighters are out they need to be controlled, again a CIC job or that of an AWACs if the operations are extended.
Finally, let’s consider the ship itself. Are we talking a battlecarrier (i.e. a battleship with aviation assets), something that is capable of dishing out damage, take a punch and still launch fighters? Because this means heavy weapon mounts, armour, shields, heavy duty engines and increases the likelihood that fighters will be launched under combat conditions – do you really want to open massive doors when there are torpedoes flying around?. Are you talking a standoff carrier (i.e. a dedicated carrier vessel like a CVN)? Because this isn’t meant to go into combat and so can get away with reduced armour and defences and minimal speed and agility, instead relying on overwhelming fighter and fleet support to keep it safe. Or are you thinking something along the lines of an escort carrier? Something fast and nimble enough to keep up with a fleet and out of the worst trouble, but with a small air wing sufficient for close range defence to supplement the capabilities of the fleet or convoy its escorting. All three have their place, all three will look very different.