How can I enable connection state handling of all devices, by default during auto-discovery process?

I would like to setup the system to enable connection state handling of all interfaces during the autodiscovery process. Any ideas how I can do that?

You can do this by creating a device template yourself, from a device with one SNMP Traffic Sensor in it, with the Connection State Handling Setting configured the way you want it to. The reason to have only one SNMP Traffic Sensor in the device (from which you create the Template from), is that only the first one of this sensor type is written into the template (further one, when the template is then used for the Auto-Discovery, still all interfaces with traffic counters above 0 will get SNMP Traffic Sensors added).