If using the official web interface, all bots, who was running, will be started again after restarting the main JTS3ServerMod process. If you have very much bots, it may take a while, because the JTS3ServerMod only starts 10 bots per second (default setting).
If not using the web interface, make sure that the bots are enabled by setting a 1 at:
MySQL table jts3servermod_instances column enabled
File JTS3ServerMod_InstanceManager.cfg at X.instance_enable