Detecting affiliate links/redirects?

Yes, usually it will.

There are a few exceptions: if PHP is running with open_basedir or safe mode enabled, the plugin may not be able to follow redirects. Also, some older versions of the Curl library have a bug that causes problems with redirects.

To check if the above applies to your server, go to Settings -> Link Checker and click “Show debug info”. This will display a bunch of details about the server and PHP configuration. The plugin will highlight any problems it detects in yellow.