That's the point of the sub-hubs - you connect to them instead of the main hub, and the sub-hubs themselves are connected to the main hub. Limits number of connections to the main hub while providing a distributed and organized connection system, with the side benefit of being able to theme the sub-hubs to the local player bases that are connected to them. This concept isn't all that new - it's actually used commonly in communications networks and networking infrastructure. Software implementations include standards such as IRC. The reason this method is used is because it plain just works better. Distributed load across multiple systems is a good solution to problems such as this, and has the nice benefit of allowing a lot more player customizability in minecraft just because there is less physical space needed and used.
If you want to make the system even more cohesive and reusable/sustainable you can chain the sub-hubs together in a loop and avoid a central nether hub all together, which allows for even more benefits and a immersive network to be explored by players.
The reason for doing this is simple: Prevention of cluttering and unusability of nether space and hub space, while providing an opportunity to act as a blank canvas for players to demonstrate their creative side.
Of course it would be a large undertaking to convert a preexisting system and the unfortunate situation is that most players do not tend to clump their base locations often, so there may be a few sub-hubs required, but if players are able to cohesively and properly add their own sub-hubs to the sub-hub loop then the system is infinitely expandable while maintaining effectiveness.
Of course the preferred method of sub-hub connection would be rail systems powered by rail pressure plates as to prevent lag. This also allows for the opportunity to allow the players that are interested (most certainly myself) to build a train network.