BUG: groupby dropna for multiindex dataframe 
- [x] I have checked that this issue has not already been reported.

- [x] I have confirmed this bug exists on the latest version of pandas.

- [ ] (optional) I have confirmed this bug exists on the master branch of pandas.

---

Hello,

I'm not sure if it's a bug report, a feature request, or if there's already another way to do it. In which case, I would be happy to hear it and close this issue.

#### Code Sample, a copy-pastable example

```python
import pandas as pd
import numpy as np

test_df = pd.DataFrame.from_dict({
'gene_1' : ['Bacteria', 'Lactobacillus', 11, 17],
'gene_2' : ['Bacteria', 'Lactobacillus', 9, 3],
'gene_3' : [np.nan, np.nan, 1, 2],
'gene_4' : [np.nan, np.nan, 3, 4],
'gene_5' : ['Bacteria', np.nan, 10, 11]
},
orient='index', columns=['kingdom', 'genus', 'sample_1', 'sample_2'])
test_df = test_df.set_index(['kingdom', 'genus'])
```
![test_df](https://user-images.githubusercontent.com/22837825/95197623-2cc05800-07da-11eb-9d9e-7bfead83ac54.png)

```python
test_df.groupby(level=[0,1], dropna = False).sum()
```
#### Current output

![groupby sum](https://user-images.githubusercontent.com/22837825/95197644-32b63900-07da-11eb-9dd4-603f0c35f367.png)

#### Problem description

I would like the dropna option of groupby to handle multipleindex dataframe

#### Expected Output

![whatiwant](https://user-images.githubusercontent.com/22837825/95197703-4b265380-07da-11eb-976f-d1c2f48ccb7d.png)

#### Output of ``pd.show_versions()``

<details>

INSTALLED VERSIONS
------------------
commit           : db08276bc116c438d3fdee492026f8223584c477
python           : 3.7.3.final.0
python-bits      : 64
OS               : Linux
OS-release       : 5.4.0-48-generic
Version          : #52-Ubuntu SMP Thu Sep 10 10:58:49 UTC 2020
machine          : x86_64
processor        : x86_64
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.1.3
numpy            : 1.19.2
pytz             : 2020.1
dateutil         : 2.8.1
pip              : 20.2.3
setuptools       : 40.8.0
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : None
psycopg2         : None
jinja2           : 2.11.2
IPython          : 7.18.1
pandas_datareader: None
bs4              : None
bottleneck       : None
fsspec           : None
fastparquet      : None
gcsfs            : None
matplotlib       : None
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : None
pytables         : None
pyxlsb           : None
s3fs             : None
scipy            : None
sqlalchemy       : None
tables           : None
tabulate         : None
xarray           : None
xlrd             : None
xlwt             : None
numba            : None

</details>

Related issues : #3729 #29716

Thank you,

Agnès
