If you are not able to delete a "Native" Azure AD registered application because of inactive "delete" button in the Azure Portal, there is a solution.
Just edit the app's manifest and change "availableToOtherTenants": true to "availableToOtherTenants": false.
The issue is that there is no "Multi-tenanted" switch in the "Native" application's blade in Azure Portal. "Web App / API" application has it.