I mean it would make sense mathematically to ensure that all planets could be defended by at least 10 ships. To have less than 20,000 ships leaves the Federation completely defenceless throughout the majority of its territory.
I don't think this would work. Even if there were 20 ships per planet, or 50, or 300, they would still be defeated by the 1000-strong invasion fleet of the enemy, while the tens of thousands of other Starfleet ships would be uselessly scattered elsewhere in groups of 10, 20, 50 or 300.
It would seem much more practical to have a 2000-strong force that could be sent to wherever the enemy is sending his 1000-strong one, and to keep some 99% of the Federation undefended as long as the enemy isn't going there. After all, the Trek players would have a pretty good idea of where the enemy was making inroads, and could intercept the foe near the borders, rather than having to control the whole internal volume. Trek ships just aren't fast enough to take their opponents completely at surprise, except in exceptional circumstances.
Cloaked forces might penetrate for small-scale raids, perhaps to be met by local defenses, but those wouldn't be able to perform "proper" invasions which apparently still require a logistics chain. A fleet in being, deployed where the enemy can't get at it, but ready to pounce at him, would be the most practical way to defeat a Trek-style foe.
Timo Saloniemi