If the value of the Hyperlink field is pointing to an object within the current SharePoint site, the SharePoint front end will automatically update the URL for the AAM site you are currently using. BUT if you are pulling the value programmatically it will always default to the URL of the default AAM site.
Better Way to Fix:
I discovered an even better to fix this problem and it all has to do with how you open your SPSite Object.
For example if you do
SPSite site = new SPSite(SPContenxt.Current.Site.ID)
It will open the site in the default zone, which will then always return the URL of the default zone.
But if you do the following:
SPSite site = new SPSite(SPContext.Current.Site.ID, SPContext.Current.Site.Zone)
It will open the site in the zone the user is currently in and return the correct URL.