You can archive a project from the "Projects" tab of your workspace. Hover over a project and select "Archive Project" under the options menu:

Zeplin's Summer Breeze release has a new options button near the project name where you can manage your project, including archiving it.

Archived projects are stored in the cloud but not accessible to you or your teammates. You can reactivate them anytime as long as you have a subscription with enough project slots.