I would like to be able to exclude a whole list or folder from the Timesheets.

Why ?

There are no duration custom field, so sometimes as a workaround I am using time estimate and time tracking to duration entries. But they have nothing to do in my actual timesheets.

If duration existed (asked here https://feedback.clickup.com/feature-requests/p/new-custom-field-type-duration), I wouldn't need that and could eventually automate that : if time is tracked (because it can be easy to record the time too) it would fill in the duration field and automatically erased tracked time entry afterwards.