By that point - if not earlier - you really need to start asking yourself what you're gaining by using a CV or CF rather than a more conventional raider with a few seaplanes.
What better way to explore the ideas then to run them in a simulation! Like Rule the Waves 2!
I suggest that going to 10,000 tons is missing the goal of cost effective raider. You could almost build 2 of the others and thus kill twice as many merchants. Having twice the firepower needed to kill one merchant doesn't help as their are no bonuses for twice-dead.
In terms of the plane's avgas, spares and munitions RTW2 has them in the tonnage used for the plane that far exceeds the plane's weight. Needs for ammunition, fuel and food are an issue for any raider, conventional or not. Graf Spree did what it did in WW2 because of the Altmark. Planes carried in a transport ship as cargo can be deck managed by the Aviation carrier's cranes and its not hard to imagine the transport, or the flat top, having at least one plane-capable crane to stock up the flat top CVLR without needing a flying off deck on the transport.
On an information addition I noticed the AVR I'm building have an ASW of 0 while the CVLR has a rating of 2. So the flat top with torp planes actually is contributing ever so slightly the to the war's anti-submarine effort. Would prefer if the game gave the AVR 1-2 points for its planes though.
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For consideration and debate:
In terms of comparison lets call the conventional raider with a few seaplanes a CLR, the flat top mini carrier the CVLR and the seaplane aviation raider AVR. Putting a + for an advantage and a - for a comparative weakness major points (in game and/or if really built) for comparison are:
CLR:
+ light armor
+ decent guns
+ can conventional fight an intercepting CL if caught
+ can act as a forward scout in a fleet battle
+ few seaplanes for scouting (like 2 or 3)
- highest build cost of the options
- can't fight a CA or bigger if caught
- little to no over the over horizon attack power
- obvious warship
- would have to stop for air handling ops
AVR:
- little or no armor
- moderate guns possible but not much armor
- can't fight CL or CA so should run on all "unexpected" forced encounters
+ a few or more seaplanes (2,3 up to 5 or 6)
+ lowest cost
+ looks like a merchant so has the best ability to hide
+ looks like a merchant so might trick its way into getting fuel and food, but not weapons nor planes, resupplied at neutrals
- would have to stop for air handling ops
CLVR:
+ only one of these with an over the horizon attack power
+ torp planes could make an attack on a CA, maybe (only one of the 3 with a plausible chance)
- obvious warship, hard to fake being anything other than a carrier
+ Can fly planes in more weather states than the CLR or AVR
+ Can bomb land targets far inland (not represented in RTW2)
- limited guns
+/- option to build with a little armor and some bigger guns
- moderate cost (needs verifying especially with regards to the cost of the planes)
+ Largest air group so can make the largest searches for targets
+ Can provide planes in fleet actions
There isn't anyone absolute always best so far. The cost-to-benefit isn't well referenced yet.
Also bear in mind that technology in each game will affect things. At one point only float planes are available making the CVLR not even possible. Without bombs on the floatplanes the CLR has a better case except for the way the AVR could still hide as a normal merchant and the AVR likely costs less.
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Edit:
Sample CLR
6,100 tons, ~22,000 cost to build, 28 knots speed, long range oil fuel
4 x 6 inch guns (2 fore, 2 aft), 8 x 4 in DP (4 to a side), 2 underwater torps (1 p/s), various AA
Belt armor 2.5 in, light armor on 6" main turrets and 1" shields on 4" DP secondaries
2 floatplanes in hanger
cost to build 22,000 (the armor is expensive)
Cost comparison of the samples I've provided
AVR 16,000
CVLR 19,500
CLR 22,000
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Edit 2:
Summary so far:
Most cost effective sea raider: AVR
Most adaptable and expensive: CLR
Best over the horizon ability: CVLR