After much research and implementing ton of added scripts on my apache server to track it - the bots did effect the shutdown. However, for this not to happen to you or if you ever have a problem of that nature this is how I resolved it.
It is an excellent article about how to implement the script to restart immediately once all available threads for apache are exhausted and your apache crashes. The script basically check apache server status every 5 min and in an event that it crashed - it will automatically restart it and send you an email notification. I say pretty good deal for risking to be offline only 5 min if anything major happens. Just as well I am also running a cron job every morning at 1am to restart apache. Please note that you need to have knowledge of SSH commands and manipulations in order for this to happen. And OMG I am talking like a geek... All the best to you...