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Can't comment much about the docker side since it's not something I'm familiar with.
For the kernel part, assuming what you're referring to as UUIDs is the pid namespace mechanism, I'm failing to see how that would add overhead with containers. The namespace lookups/permission checks are performed regardless of whether the process is in a container or not. There is no fast path for non-containerized processes. The worst overhead that this could add is probably one extra ptr chase in the namespace linked list.