Well, high deployment cost is generally more punishing than a high maintenance cost simply because the player is probably going to get into multiple battles per month. This change would mean that Scy ships are slightly more supply-efficient if you only fight once a month, on-par if you fight twice a month, and slightly less supply-efficient if you fight three times a month. Without having played with it yet, I'd guess that the numbers are too small to make that much of a difference in terms of supply costs.
That's not exactly how it work: the ships do not consume their monthly cost while recovering CR, that make the relative importance of Deployment cost and Monthly cost highly dependent on your CR recovery and repair rate, and tend to make the deployment cost more important. But that's why the difference with vanilla is twice as pronounced for the monthly cost than for the Deployment cost.
If on average a early game fleet get back to full CR in 4 days, not taking into account the individual ships repair rates and that they are often helped by stations repairs, given the difference between the new costs that means the fleet start to get more expensive than vanilla if you deploy ALL ships more often than every 19 days on average. If a mid game fleet needs 8 days, it becomes more expensive if you fight more than every 23 days. Those average are not that easy to reach: as soon as you start traveling in hyper to hunt bounties, you can very well deploy far less often than that. That makes the early game a bit easier because of the reduced cost, while encouraging even more than vanilla to not over-deploy. And late games the supplies are less of a concern anyway.
Also when I say "above vanilla", I'm talking about the cost of a ship of similar tier. And Scyan ships are not very high tier.
However, this does mean that fully Scy fleets are going to be at a slight disadvantage in terms of deployment points in the extreme late game. If you have a fleet with combat ships worth more than 40% of the battle size in DP, and you're in situation where you're massively outnumbered by a non-pirate fleet and need to deploy as much as you can just to survive, you're not going to be able to deploy as much as you used to be able to. At 300 battle size, SSP default, you'll be down approximately 11 DP or about one destroyer or two frigates. This will also affect AI fleets; if you're being menaced by a gigantic pileup of Scy fleets, they'll be deploying about 16 fewer DP worth of ships at a time. That's probably going to be the biggest effect of this change.
That is of no consequence because as you said the repartitions of deployment points between both sides is made after the relative strength of their fleets (calculated from their deployment cost), meaning while the Scyan ships need 10% more point to deploy the same amount of ships, the fleet also get 10% more points to spend.
In addition to that, the next SS+ update bring some changes to the way the maximum fleet size is handled that may give Scyan fleets a tiny advantage.