).Re. the gnome updates, you are probably using one or more gnome apps in your xfce installation, thus the gnome. It is rather common to use gnome apps in kde and kde apps in a gnome setting.
Re. the Ubuntu updates, Mint is core based on Ubuntu. Basically, I believe the developer's of Mint started with Ubuntu-Kubuntu-Xubuntu and built Mint from that point forward (like why re-create the wheel if you don't have to). Don't mis-interpret this as there are marked differences between the two distro's... that's why we're using Mint vs. Ubuntu right?
Re. whether to use the updates or not, that's entirely your call. The updates either fix something that's not correct, or roll improvements in the app. If the update addresses an app problem, not doing the update may lead to a run time error on the application. I would recommend a disciplined approach to doing the updates. Set some time interval and stay with it.
Things can go wrong on rare occasions with updates. From my experience, I would say that is the exception rather than the norm. There are a number of things that you can do to minimize the effects of updates gone bad. If you're interested, check out my web site in the Linux section under a Backup Strategy for one possible approach.
Hope the above help.
DataMan