This is by design as in AEM the inbox implementation allows the user to take action one item at a time.
This is not supported in the new inbox which is a unified inbox view of different "task" types including Workflow notifications, Project Tasks, Ad-hoc task and AEM Form task assignments. Prior to 6.3, each of those had their own "inbox" view - 6.4 inboxes unified all of those.
The issue is the Inbox is different from the notifications. Previously all items in Notifications.html are work-item types only. Now with the unified inbox, the item types are different, and each has different individual actions that can be performed on them.
This is being tracked as an improvement in 6.5 (CQ-4230313) to support multi-select in the inbox, but it's a non-trivial improvement.