The Pending email is only sent if email confirmation or user approval is enabled. The Welcome email is always sent when the user is active and can login (after confirmation and user approval).

If customizing the pending email either via the parameter or language override and you have confirmation enabled you need to be sure to use the [CONFIRM] substitution so the link is included in the email. There is no reason for it to be missing in a default clean install of CB and have confirmed as much.

If it's missing it's because the user has no confirmation code, the language string was overridden and missing the substitution, the parameter was changed and missing the substitution, or worst case the mail provider is filtering it out.