While this does not mean that the entire contents of the folder are being re-indexed (that only happens the very first time the folder is unlocked), it can still be annoying, especially if you have many folders set to autounlock when you login.
Thankfully, turning off this behavior for a particular folder is simple:
1. Open the Spotlight preferences and click the Privacy tab:
2. Unlock the folder and open it in the Finder.
3. Click and hold the mouse button down on the folder icon in the toolbar until it changes color, then while continuing to hold down the left mouse button, drag it onto the Privacy list:
That's it. To re-enable Spotlight support for that folder simply remove the folder from the Spotlight privacy list.