I want to reduce the spawn rate of these mobs, but my settings do not seem to be having any effect; they are still spawning in large numbers.

config\incontrol\spawn.json

[
{
"dimension": "minecraft:overworld",
"mob": "subnautica_flow:skyray",
"mincount": 1,
"maxcount": 2,
"result": "deny"
}
]

What this rule does is the following:

• For the mob 'skyray' if there is at least 1 mob and maximum 2 mobs it will deny the spawn.
  That means that if there are more then 2 this rule will not fire since 'maxcount': 2 condition is not satisfied.

So in summary: remove 'maxcount': 2