According to the Tfl website the last trains to Waterloo from Bank on Saturday are at 00:06, 00:16 and 00:26 Sunday morning. Assuming that you are travelling either today or next Saturday, there are no planned engineering works affecting the Waterloo & City line.
Be aware though that the subway between the Northern Line/DLR and Waterloo and City Line is currently closed so the interchange time will be longer than normal. It might (but check) be quicker to change at London Bridge for the Jubilee Line.
The essential things in life are seen not with the eyes, but with the heart. --Antoine de St. Exupery