Due to a large number of virtual hosts, you want to have a single logfile and split it up afterwards.
LogFormat "%v %h %l %u %t \"%r\" %>s %b" vhost CustomLog logs/vhost_log vhost
Then, after rotating your logfile:
split-logfile < logs/vhost_log
The LogFormat directive in this recipe creates a logfile that is similar to the common log file format but additionally contains the name of the virtual host being accessed. The split-logfile utility splits up this logfile into its constituent virtual hosts.