Yes, missing natures / facets will prevent some features from working as they should.
Can you tell us how you created the project – was this something that was created in MyEclipse or is just a Maven project (or other) that you are trying to import into MyEclipse? Normally, if you import a Maven project into MyEclipse, a migration wizard will show up, allowing you to update the project with the necessary natures and facets.
Here are a few things you could try:
1) Open the migration view in MyEclipse and see if the project is listed for migration. If so, go ahead and migrate the project.
2) If this is a Maven project, choose Maven > Update Project from the project’s context menu
3) As a last resort, you could create a new EJB project within MyEclipse with the correct Java EE version (that corresponds with your project). This project will have all the metadata you need. You can then copy all your project’s source into this project, while keeping the metadata untouched (renaming it ultimately to have the same name / location as your original project)
Please let us know if this works or if you need further assistance.