You should check in an Xcode 5 .xccheckout file; in general, files in xcshareddata should be committed.
An .xccheckout file contains metadata about what repositories are used in a workspace. For a single project in a single repository that doesn’t make much difference. But if you’re using a workspace that has multiple projects from different repositories, the presence of an .xccheckout file in the workspace allows Xcode to know what all of the components that make up a workspace are and where to get them.