Pandas count null values in a groupby function

I think you need groupby with sum of NaN values:

df2 = df.C.isnull().groupby([df['A'],df['B']]).sum().astype(int).reset_index(name="count")
print(df2)
     A      B  count
0  bar    one      0
1  bar  three      0
2  bar    two      1
3  foo    one      2
4  foo  three      1
5  foo    two      2

Notice that the .isnull() is on the original Dataframe column, not on the groupby()-object. The groupby() does not have .isnull() but if it would have it, it would be expected to give the same result as with .isnull() on the original DataFrame.

If need filter first add boolean indexing:

df = df[df['A'] == 'foo']
df2 = df.C.isnull().groupby([df['A'],df['B']]).sum().astype(int)
print(df2)
A    B    
foo  one      2
     three    1
     two      2

Or simpler:

df = df[df['A'] == 'foo']
df2 = df['B'].value_counts()
print(df2)
one      2
two      2
three    1
Name: B, dtype: int64

EDIT: Solution is very similar, only add transform:

df['D'] = df.C.isnull().groupby([df['A'],df['B']]).transform('sum').astype(int)
print(df)
     A      B     C  D
0  foo    one   NaN  2
1  bar    one  bla2  0
2  foo    two   NaN  2
3  bar  three  bla3  0
4  foo    two   NaN  2
5  bar    two   NaN  1
6  foo    one   NaN  2
7  foo  three   NaN  1

Similar solution:

df['D'] = df.C.isnull()
df['D'] = df.groupby(['A','B'])['D'].transform('sum').astype(int)
print(df)
     A      B     C  D
0  foo    one   NaN  2
1  bar    one  bla2  0
2  foo    two   NaN  2
3  bar  three  bla3  0
4  foo    two   NaN  2
5  bar    two   NaN  1
6  foo    one   NaN  2
7  foo  three   NaN  1