Does upgrading to Mountain Lion means I have to reinstall Android SDK and Eclipse? I'm on Lion and am learning Android development. I have Eclipse Indigo Service Release 1 version and the lastest SDK installed.

If I upgrade to Mountain Lion does it mean I have reinstall the SDK?

I have folders in the root Macintosh HD such as android-sdk-macosx, are these deleted?
No, nothing is deleted when updating. A common sense would be to back-up everything as things can go wrong, but if everything go right, nothing is deleted! Even opened apps are reopened after update.

It must be noted though that the first time you launch Eclipse, OS X will tell you that it will install Java first, as Java is not installed by default anymore.