Upgrading is very doable and easy. However, Jfrog is currently down so if you try to do so right at this moment you’ll get errors about not being able to install the add-ons. You can get around that short term by downloading the add-ons .kar file. See Jfrog repo is down, can't install OH nor add-ons - #44 by rlkoshak for details.
To upgrade your container, simply pull down the latest release Docker image and spin up a new container using the same parameters as your old one. The container will run a script that notices that your config is for an older version and, after backing the configs up of course, make any changes necessary to bring the config up to that version of OH.
The number of differences between OH 3.1.0 and 3.3.0 release is pretty minimal from a config perspective. But it would be a good idea to look at the release notes for 3.2.0 and 3.3.0, paying particular attention to any mention of “breaking changes”.
Having said all of that, there can be some benefit to starting over from scratch as well. It lets you fix stuff that is hard to fix after the fact like Item names and naming patterns and the like. So it’s up to you.