I wonder if overnight radio repair somehow screws things up for your zwave network. I've looked at the logs from your hub several times over the last few days, even ramping up log level to make sure nothing untowardly is happening. There's definitely not enough going on to explain the slowdown, yet the pattern is things grind down to a crawl overnight.
I'm going to add some sort of a switch to disable nightly radio cleanup, but in the meantime let's just have your hub reboot itself after that radio repair job runs. Below is a link to one thread with instructions to set up reboot @ 4am. This is totally a band aid, but you should have a working setup while we're putting together a solution.
