I feel like just looking at the cost ultimately converted into credits misses some important nuance. First of all, 350 extra crew, yeah, that's an extra 35 supplies per month when converted to credits, but it's not supplies that need to be carried with you, it's just credits.
This is true. I can buy supplies on a discount or win them in a battle, but, I can never do anything to reduce the salary. And it's maintenance costs aren't just in the same ballpark as Paragon's, it's more expensive than it. Slightly more without any fuel usage, significantly so with. Same goes for Legion. Onslaught becomes cheaper only after 3 monthly deployments, if I recall correctly.
A small detail I just thought about is that all ships lose CR at the same rate, but not all ships require the same amount of supplies per CR. I don't know how often it affects players (especially new players who don't know it's more efficient to redeploy, instead of burning CR), but it makes burning CR on low-tech ships an expensive endeavour. Well, more expensive than usual CR burning.
You can actually pay less salary. Just don't fill your ships to minimum crew. You take a CR penalty, but as long as you stay above 40% you won't have malfunctions. Its not a good option, but its there if you desperately need to trade some fleet effectiveness for a bit of cash. I may have some minor experience with this due to playing spacer starts and running the very first real ship I get my hands on under crewed.
As for supplies on discount, I feel like there's a lot more places where supplies are more expensive than 100 credits rather than less. Of course that also means extra supplies you get from your victories can be converted to cash to pay for crew. To be honest, if you're hauling around capitals, I feel like 2,000 or 5,000 credit differences here and there don't really matter in the grand scheme of things. Certainly you can spend a lot more credits hunting for a good deal instead of simply buying the closest and immediately heading out to the next bounty or target. Capacity matters, for determining your reach but 4 destroyer class tankers will still get a bunch of Onslaughts and Legions from the core worlds to the edge of the sector and back. Losing a frigate or a destroyer in battle is a bigger deal in terms of cost.
As for deployment costs assuming base prices, Onslaught ties or beats a Paragon in terms of crew/supply costs at one deployment.
Onslaught's 750 crew is 7500 credits per month, plus 40 supplies valued at 100 credits each is 7500+4000=11,500 credits per month. 1 deployment costs 40 supplies, or effectively another 4,000 credits, so 15,500 for 1 deployment per month.
Paragon's 400 crew is 4000 credits per month, plus 60 supplies, so 4000+6000 = 10,000 credits per month. 1 deployment costs 60 supplies (6,000 credits), so 16,000 credits for 1 deployment per month. Skills of course affect this, with -25% less supplies being worth more on a ship with a higher supply/crew ratio (like the paragon). That shifts the base sitting there cost to 10,500 credits versus 8500, so they exactly tie after just 1 deployment. Onslaught always comes out ahead at 2 deployments a month ignoring fuel and not going over base deployment time.
Hmm. I wonder if a "Low Maintenance" hullmod (that would, say, halve the monthly supplies but not the deployment cost) on the Onslaught might not be an interesting change. Or, could slap "High Maintenance" on the Paragon, that could be... fun. And thematic!
Low maintenance doesn't do much for the Onslaught, since the majority of its upkeep cost comes from crew salaries. 7500+2000 = 9,500 vs normal 11,500. About a 18% shift in upkeep assuming you're just sitting there in space. If you're burning to the edge of the map and back, its even less (burn 20, 2 light years per day, 60 light year round trip) is 900 fuel or 22,500 credits. 32,000 vs 34,000 isn't really noticeable I think.
High maintenance on a Paragon is a bigger deal, doubling 6000 credits to 12000 credits per month, so 10,000 to 16,000 for about a 60% shift in upkeep costs (again ignoring fuel). If you do assume you're flying out to the edge and back over the course of a month (burn 20, 2 light years per day, 60 light year round trip is 1 month), that 600 fuel or 15,000 credits at 25 credit per unit. In which case 31,000 over 25,000 is only a 24% increase in credit running costs. Less if deployments are included.
Most players I would imagine would still pay that for a Paragon. I certainly would. I mean, I run my end game fleets at full crew. Which means I'm literally throwing credits out the window and it doesn't really affect my bottom line significantly. Especially at the point in the game that you can generally acquire a Paragon. Unless they're composed primarily of Paragons, I don't see most end game fleets caring actually changing composition with that change. Maybe you throw in an extra destroyer or cruiser freighter for a quad set of Paragons?