Impact of Netflow accounting
A few days ago I was describing the impact of CEF accounting on a router (based on its architecture). The picture is clearer with Netflow: Cisco has published a white paper detailing the impact of various types of Netflow accounting on a large variety of platforms, from an 1800 ISR to the GSR (12000).
The link to this white paper has been published in Joe Harris' blog.
You could, however, use Netflow to figure out the top flows that cause the high CPU utilization. I would also log incoming ACL failures to see whether you're under a DoS attack.