BUG: .value_counts converts pd.NA to np.nan

[JarnoRFB]

• I have checked that this issue has not already been reported.

• 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.

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Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Code Sample, a copy-pastable example

pd.Series(["a", "a", "b", pd.NA]).value_counts(dropna=False).index
Index(['a', 'b', nan], dtype='object')

Problem description

.value_counts converts pd.NA to np.nan. Instead pd.NA should be preserved. In my use case, I use value_counts to find small groups, based on which I want to filter the data. This is hard, if the value in the counts differs from the actual value.

Expected Output

Index(['a', 'b', <NA>], dtype='object')

Output of pd.show_versions()

INSTALLED VERSIONS

commit : c7f7443
python : 3.7.9.final.0
python-bits : 64
OS : Linux
OS-release : 5.4.0-80-generic
Version : #90-Ubuntu SMP Fri Jul 9 22:49:44 UTC 2021
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 1.3.1
numpy : 1.20.2
pytz : 2020.5
dateutil : 2.8.1
pip : 19.3.1
setuptools : 49.6.0.post20210108
Cython : None
pytest : 6.1.2
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 2.11.2
IPython : 7.16.1
pandas_datareader: None
bs4 : None
bottleneck : 1.3.2
fsspec : None
fastparquet : None
gcsfs : None
matplotlib : 3.2.1
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : 3.0.0
pyxlsb : None
s3fs : None
scipy : 1.4.1
sqlalchemy : 1.3.13
tables : None
tabulate : 0.8.7
xarray : None
xlrd : None
xlwt : None
numba : None

[MarcoGorelli]

Thanks for the report, can confirm this reproduces on master

[phofl]

related to #33066 and #32931

This would vanish with an extension dtype