With VMs, you can use the same tools you use with any other machine.
With containers, you are responsible for figuring out which ones need which packages and how to re-build them. Your method is likely to be idiosyncratic, so you not only need to be your own security team, you need to be your own packaging maintainer and infrastructure maintainer.
The two extreme versions of this are the neglect model, in which you just don't care about anything, and the bleeding-edge model, where you automatically build with the latest versions of everything pulled from their origins. Both ways end up with unexpected security disasters.