Andy,
You should be able to rename your EJB3 Projects to end in an EJB3 extension, that will create a file.ejb3 resultant archive (we did this for the other JBoss archive types like RAR, SAR, etc).
Also what we have planned for 4.0 is to instead of using the project name, expose the already existant “archive” value from the .mymetadata file in EJB files and allow the user to enter a name of the archive that the project is deployed as, which will give maximal flexibility.