Hi Craig,
If I am understanding correctly you could probably do this in a few ways. Some easier than others. Work modes for that system/systems getting the DB upgrade, and set the mode for when they will be down. It sounds like you are getting errors at night that you don't want, which these work modes can be used for that as well. SolMan would stop aggregating alerts for those systems. Lastly I would say to just shut down the SMD agent on the managed system while the upgrade occurs - though I am not sure if other experts would advise this as there may be easier ways.
Zach