|I'm assuming the noise is coming from a cooling fan.|
If it's a laptop it may be powering down--not going into standby or hibernaton but slowing down the cpu--during periods of low usage. The cooling fan is probably slowing down too. Then when the updates start coming in the cpu and fan speed up again.
If you want to be more in control of when (or if) you get the updates, you can turn off 'automatic updates' in security center in control panel.
DAVEINCAPS - Made with REAL high fructose corn syrup.