Whenever changes have been to the repository (see https://gerrit.wikimedia.org/r/#/q/project:labs/tools/discordwiki
), it is indeed better to archive the repository. Else all the review comments, approvals etc are lost :]
When a repository is empty, feel free to delete them. The issue there is just some warnings logged on the server side and are not really causing any issue. The deletion plugin needs to be fixed and then some database fields would need to be updated, but that is about it.