Hi Derek, you can have either have SMTP or Database notifications, not both.
So if they are logging on to EPDM, then the notification system needs to be set to Database.
Once that has been done, they should receive notifications straight to their EPDM inbox, and links should work as you state above.
I usually recommend 2 different approaches to manage how your users are triggered to action.
1) Use the database notification system for your users who are inside the building a majority of the time then use an API add-in to relay emails via SMTP to notify users who are on travel as a complement. If they travel, they won't get the database messages but will get an email by the add-in while on the road.
2) Avoid email notifications altogether and use live EPDM Dashboards. See my website "Services" page for a brief video on an innovative approach to an EPDM implementation using EPDM Dashboards.
Let me know if my consulting services would be a benefit to your organization.
Hope this helps,