We just ran into the same problem with adding a link in a marketing email to a Microsoft Office 365 Bookings function (where the person can pick a meeting time directly from a subset of the sales person’s Outlook calendar. The parameters break the link.
Making this a GLOBAL setting for all emails is lazy coding. Hubspot could certainly add a checkbox to the “edit link” dialog box and on the email settings page, even if it only works to untrack a link or particular email.