You can easily only update selectively, but your "updates" list in the Play Store does get littered with notifications for all the apps you do not want to update. It used to be possible to "disconnect" them from the Play Store, but Google changed the way that worked a few years ago.
Apps you don't use should generally just not run. If they are pre-installed and not uninstallable you should in most cases just be able to disable them (which also clears their data, removes any updates, and ensures that you don't receive any further updates unless you re-enable them).
So when and why to root? When is "when or if I want to/have a reason to". Why: is there anything you want to change that requires root? If so, that's your why. Root makes a number of things more convenient, allows you to make changes such as removing system apps, deeper theming, better backups, firewalls and more comprehensive ad-blocking. Some apps also don't work if they can detect that the device is rooted, particularly banking/payment apps and some media apps (some rooting methods can hide from some of these apps, but if any of this is important to you then check first).