Вы можете установить одинаковые даты в datetime:
hurricane_df['datetime'] = pd.to_datetime(hurricane_df['datetime'].dt.strftime('%H:%M:%S'),
format='%H:%M:%S')
print (hurricane_df)
identifier datetime
0 AL011851 1900-01-01 00:00:00
1 AL011851 1900-01-01 06:00:00
2 Al011851 1900-01-01 12:00:00
Или преобразовать столбец в timedeltas:
hurricane_df['datetime'] = pd.to_timedelta(hurricane_df['datetime'].dt.strftime('%H:%M:%S'))
print (hurricane_df)
identifier datetime
0 AL011851 00:00:00
1 AL011851 06:00:00
2 Al011851 12:00:00
hurricane_df = hurricane_df.groupby('identifier')['datetime'].diff().fillna(0)
print (hurricane_df)
0 00:00:00
1 06:00:00
2 00:00:00
Name: datetime, dtype: timedelta64[ns]