These additions are upgradable as long as you are using the Kentico UI to do so. In fact this is how it was designed. There are some considerations you need to look into, if you ever have a need to have a single user authenticate against different sites or sections within the site which have different properties. In this case you might want a custom table with a FK relationship back to the Users ID/GUID and store their preferences in the custom table.
If you don't anticipate that need or any other scenario in which you might need to have more than one set of user preferences, then you should be ok leaving them as additions to the user.