No doubt many answers but here's what I do.
I have a staging/dev server that is identical in OS and setup to a Production server. (I use it to test updates to my app though). I will do the package updates on that box and test, then if all well (and truth is it has never failed on me yet!!) then a few days later I upgrade the prod box.
sudo apt-get update will update the list of repos etc. sudo apt-get upgrade will perform the updates etc.
It will/can affect your app etc.
The only issue I have with Ubuntu on forge is the constant requirement to restart for the security updates whereas my non-Forge AWS flavor linux hasn't needed a restart since I've had it!