Eclipse isn't an
IDE it's a framework. The most popular Eclipse spin has a
Java IDE implemented as pre-installed plugins. The plugins implement Perspectives and Views. So Eclipse itself doe not understand "projects". Instead you have to deal with a project plugin.
When you close a Java project, its primary function is to hide the project resources, The project is only closed, not deleted, because you can later re-open the project.
If you really want to delete a project there's a separate Delete project option on the menu. Note that a project consists both of a directory and the
.project file that defines the specifics of the project. And that a project can live anywhere on your filesystem. The Workspace is a logical organizer, not a physical parent directory as such, though the workspace directory does create project directories within itself by default.
So, when you select Project/Delete, you have the option to delete just the project definition (.project file) or the project definition plus the project's directory. Either way the project will then disappear from the workspace.