NetFlow has a reputation for increasing CPU utilization on your network devices. Cisco's performance testing seems to indicate that newer hardware can accommodate this load pretty well, but you will still want to check it out before you turn on the feature. Some symptoms of high CPU utilization are very large jitter and increased delay. Services running on the device may also be affected.
Another thing to keep in mind is the amount of data you're going to be sending across the network. Depending on how much traffic you have and how you configure it, the traffic can be substantial. For example, you may not want to send NetFlow data from a datacenter switch to a NetFlow collector on the other side of a small WAN circuit. Also bear in mind that the flows from aggregating large numbers of devices can add up.
Reference: http://searchenterprisewan.techtarget.com/tip/How-the-NetFlow-protocol- monitors-your-WAN