Is there anything that sfeik sfeika does not apply to? tumah and taharah?
There are numerous cases where sfek sfeika will not apply. To really know when it will or won’t you will have to learn Y:D 110.
The Rema Y:D 110-8 says that an item that will become permitted in the course of time will not be permitted with a sfek sfeika.
Also tuma in a private domain will apply even if there is a sfek sfeika, see mishnayos Taharos 6-4, Rambam Hil. Avos Hatuma 18-1.