NumPy is slower because it casts the input to boolean values (so None and 0 becomes False and everything else becomes True).
import pandas as pd
import numpy as np
s = pd.Series([True, None, False, True])
np.logical_not(s)
gives you
0 False
1 True
2 True
3 False
dtype: object
whereas ~s would crash. In most cases tilde would be a safer choice than NumPy.
Pandas 0.25, NumPy 1.17