In RH/CentOS atop is not being regulated by logrotate.
In /usr/share/atop/atop.daily there is an example script to deal with atop log file rotation.
The script as a find line deleting logs older than 28 days as in:
# delete logfiles older than four weeks
# start a child shell that activates another child shell in
# the background to avoid a zombie
#
( (sleep 3; find $LOGPATH -name 'atop_*' -mtime +28 -exec rm {} \;)& )
You can copy that script to /etc/cron.daily and change the number of days to 5.
( (sleep 3; find $LOGPATH -name 'atop_*' -mtime +5 -exec rm {} \;)& )