Are you saying the piped logging was already enabled on the system?
If there are more than 1000 domains and piped logging is already enabled, but you're still seeing slowness with the restarts, our team is looking into this as part of case EA-9026 to see if there is a way to get Apache to load quicker when performing a graceful restart with a large number of domains. Currently, though, I don't have any additional recommendations to provide, other than having fewer accounts on the machine.
I'm going to add this post to the internal case, but it's possible there just isn't a way to reliably speed up this work on the system.