Currently, Notification sent via Atlassian JIRA shows raw URL path when an Issue-key or a Confluence page link is included in the body of the email sent via JIRA Notification.
There is no way to control this, as in choosing if a user wants to enable Smart Links or Disable it in the emails that they receive from Atlassian Jira products.

Current Behavior:

Whenever an email is received from Atlassian JIRA products, and if the email body has a JIRA issue link then it will be always rendered as a raw URL

• Adding a comment to a ticket that triggers the email notification looks like this: (Converted to Smart Link)
  
• Receiving that email looks like this: (Issue links are not rendered as Smart links, but show up as raw URL)
  

When there are links to pasted in the email body from Confluence pages or when there is a link posted that points at a specific region in the confluence document, the URL can get very huge and that eats up a lot of space in the email body and users cannot see the information at a glance.

• Adding a Confluence Link in the Issue comment: (Converted to Smart Link)
  
• Receiving that email looks like this: (Confluence links are not rendered as Smart links, but show up as raw URL)
  

Suggestion:

Provide an option to the users to choose in their Personal Settings if they would like to receive emails notification from JIRA where if the body of the email contains a link to the JIRA issue or a Confluence page, then it can be either rendered as a Smart Link or Rendered as a normal URL path.