It maybe messages aren't sent at all so they are collecting in the queue, or it maybe they are adding faster than are sent.
If you empty the queue, the emails which were in the queue will not be sent again.
We went ahead and cleared "sys_queue_email" now the system is generating so many e-mails, about 56,901 every 12 hours. We have had to disable SMTP to prevent our users from getting spammed.
Any suggestions on how to fix this?
Most probably it's email notifications, please try disable some of the email notification in Studio > Notifications > Email