Unfortunately we're stuck between a rock and a hard place on this. We could remove the deprecated APIs but then we would need another major release in the not too distant future with Swift 6 and NIO 3, which is too disruptive for the community. And we can't keep using the old internals because it's not safe - we're already seeing issues caused with async/await because many of the assumptions of Vapor are that everything is run on the same thread which isn't the case anymore, so we need to use actors etc to make that safe. We also want to use async/await as much as possible in the whole stack otherwise adopting distributed tracing is not going to be possible.
So it's entirely a problem that we could solve but it would be more disruptive in the long term for the ecosystem to do the 'right' thing now.
To be clear - you'll get deprecation warnings when you update to whatever with the new release is and if you fix the warnings there will be no use on semaphores in any of the code you touch - it's purely there to stop us breaking the API for those who can't update their code yet but we are going to strongly suggest you migrate before deploying