In some plugins, there is a default or flag to make timeouts return as unknown – if that’s the case with your current plugin, you can filter out unknown on your notification rule.
Otherwise, it sounds like you would never want a problem notification (or at least critical), so perhaps you could filter out critical, or just skip problem notifications on the service all together.
Edit to add: you might see what is causing SNMP to timeout as well. In our environment is it usually due to packet loss (check_ping) or high resource utilization on the target. If it’s just randomly intermittent, you could also increase the timeout value (start low, by increasing 5 or 10 seconds)