I can't reproduce with a simple CustomLog "|/bin/cat >/dev/null" vhostio, works perfectly here.
Isn't your line just missing a double quote (") at the end? The last character currently is an escaped double quote belonging to the quotes around the user agent for in the log itself. Not the double quote required by the CustomLog directive.
Just reproduced your error with the CustomLog from your post and indeed results in a syntax error, even while Apache thinks everything is OK. Good news is: just added a double quote at the end of the line and as expected everything works again 
Ergo: not a problem with certbot, but with your configuration and an Apache webserver just ignoring the syntax error somehow.. Which is kinda strange..