I also have the same problem, and I wish I knew a good solution for it. I'm using DNN 4.5.5.
The email message sent out to the new users after registration is found in (Host or Admin) --> Languages --> Language Editor. It can be found in the "Resource Name: EMAIL_USER_REGISTRATION_VERIFIED_BODY.Text" field.
The URL is formed with this text: "http://[Portal:URL]/default.aspx?ctl=Login&username=[Custom:0]&verificationcode=[User:VerificationCode]"
I've tried changing the "http" to "https and I've tried changing the "http://[Portal:URL]/default.aspx" token to the actual (hard-coded) url of my portal's login page. Neither have worked...
Would love to find a solution.