Why do electric companies measure in watts, when they be measuring in joules?
No, the electric bill does NOT say "you have used 5000 Watts".  Look at it more closely.  It says that you used 5000 kiloWatt-hours.  A kilowatt-hour is one kiloWatt (1000 Watts) for one hour.  That is a measure of energy, and is the same as charging for Joules.  One kiloWatt-hour equals 3.6 MJoules.  Or put another way, they do charge by the Joule, just that they express it in more relevant units for most homeowners.