The eBweb Publisher screen displays packages that have been created in the community. It is desirable to remove old packages so that users can focus on the newly created ones more easily. Users can select (check) individual packages to delete them. But if there are too many old packages to delete then this method is not efficient enough.
The current way to delete packages is working as designed. It's just not efficient enough to do bulk deletion.
Bentley Professional Service has developed a script to delete ALL packages older than a certain age. Users can edit the script to set the deletion criteria (e.g. creation time >60 days) before running it. If needed, please open a service request and mention SR 7000806798 to obtain the script.