If you have some employees that don't need to clock in and out (e.g. salaried), you can easily disable the time clock within their profiles. This means they will not see the option to clock in at all and they will not be bothered with time clock reminders.

Under your Employees tab, choose a person from the list.

Scroll down near the bottom of the page and look for the Enable timeclock setting. Switch the toggle to No, then Save.