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Your equation converting $J$ to $Wh$ is correct for the hourly output from EnergyPlus, which could be rewritten as

$Wh_{hourly} = J_{hourly} * \frac{1 hr}{3600 s}$

If you compare the timestep output to the hourly output, you will see that EnergyPlus is already accounting for less energy consumed each timestep. For example, if the hourly HVAC electricity use was $400 J$, using 4 timesteps per hour would give a timestep output of $100 J$ (assuming constant HVAC consumption). Because of this, you should use the same equation above for converting the $J$ timestep output from EnergyPlus into $Wh$.

$Wh_{timestep} = J_{timestep}* \frac{1 hr}{3600 s}$