1. Type gpedit.msc in RUN or start menu search box and press Enter. It'll open Group Policy Editor.
2. Now go to:
Computer Configuration -> Administrative Templates -> Windows Components -> Internet Explorer
3. In right-side pane, double-click on "Disable add-ons performance notifications" option and set it to Enabled.
4. That's it. It'll permanently disable that annoying popup notification message in IE.