Sales Taxes Inactive is added as a customization to support a hybrid approach to Sales Taxes--using built-in Tax Status calculations alongside TaxJar or other automated lookup by address. Inactive blocks Tax Status entries that are replaced.
Use the Sales Taxes Search on the Reporting toolbar to find Sales Taxes you want mark Inactive. Select the rows you want to change with Command-click or Ctrl-click and then click Update to set Inactive to Yes.
In the picture this has been done for Alameda, Calaveras, and Contra Costa, which may have been replaced by CA, a TaxJar lookup for anything with a Shipping State of "CA".