Count if with a measure

What you are doing is not counting anything, but calculating your [ Count IF] measure for each line and its specific filter context in the visual. 

Try this:

COUNT IF =
VAR _T1 =
    FILTER (
        ADDCOLUMNS (
            VALUES ( Template[Facet] ),
            "@%",
                VAR _X =
                    SUMX (
                        SUMMARIZE ( Template, Template[Merged], Template[Hours by Year] ),
                        Template[Hours by Year]
                    )
                VAR _Y =
                    CALCULATE (
                        [Non Duplicate Hours Process/Activity Numerator],
                        ALLEXCEPT ( Template, Template[Function], Template[Area], Template[Name] )
                    )
                VAR _Z =
                    DIVIDE ( _X, _Y )
                RETURN
                    _Z
        ),
        [@%] >= 0.01
    )
VAR _Result =
    COUNTROWS ( _T1 )
RETURN
    _Result