As David said, you don't need to restart Agents. Just monitor your webagent log to ensure the agent has retrieved the new ACO changes.
Just to add, when you set secureUrls= yes, it is not just "target" parameter that will be removed , all the parameter will be removed and replaced with encrypted URL.
If you have multiple web agents doing SSO, then you will need to enable secureUrls in all the web agents or else the SSO fails.