You can now just delete it, assuming you don't need it for anything. Go to Window > Preferences > General > Security > Secure Storage and then click on the 'Contents' tab. If you click the Delete button and then restart Eclipse, you will no longer see the pop-up.
From what I understand, Secure Storage is mostly used with repositories like Git and SVN. In my case, I don't need it for my home computer. I use Git at work, but even so, I have never seen the Secure Storage pop up before.
Here's my solution in Nano.2 on Windows, and it's nice and easy and seems to be working:
Window -> Preferences -> General -> Security -> Security Storage
Password tab: in the Master password providers section, uncheck Windows Integration and UI Prompt
I also tried deleting the [Default Secure Storage] in the Contents tab like some other answers suggested, but this is not needed and it gets recreated upon restart anyways.
While opening the Eclipse or importing the project, you might get sometimes error called Salt must be 8 bytes long. This is because of conflicts between Java and OS key store.
Either of following are the solutions of this problem.
► Solution 1: Remove file <USERHOME>.eclipse\org.eclipse.equinox.security\secure_
storage from your system. After that please restart machine and try to use Eclipse***.
► Solution 2: Uncheck the Windows Integration (64 bit) and UI Prompt from Password tab of Windows -> Preferences -> General -> Security -> Secure Storage. After that please restart machine and try to use Eclipse.
► Solution 3: Delete [Default Secure Storage] from Contents tab of Windows -> Preferences -> General -> Security -> Secure Storage. After that please restart machine and
try to use Eclipse.