Having this many notifications is pretty unusual. It might be intentional that it doesn’t clear all your notifications, since not all 3000+ notification will appear in the dropdown when you click it. Does it get cleared down to zero when you click / refresh many times?
On the off chance you haven’t found this setting, check it out in your account settings. As a very active user, I’ve found it necessary to uncheck it:
https://www.inaturalist.org/users/edit
Also just a note that the iNat staff are in the middle of redesigning the dashboard and notification system.