Regarding the crashes, has it only crashed if a domain is actually up for renewal?
For example, with the partial log in your original post, were all of the domains Cert not yet due for renewal or did some of them actually report as doing some work?
It might help to upload the full log from that incident to pastebin or something.
If you are getting crashes even when Certbot is not actually doing any renewal work, I would maybe investigate the possibility of a different kind of resource exhaustion - ulimits (or a very high number of workers/threads configured for Apache). This is a little suspicious, but I admit it could easily be a red herring: