Yes. The files should just update in Eclipse after a "git pull" from the command line, since Eclipse is viewing editing the same files that are stored in your repo.
But a "refresh" in Eclipse never hurts, if you feel like Eclipse might not be up to date.
Also, sometimes it takes Eclipse a while to get the right little git status icons ( >, +, etc) updated after you do an operation from git bash. But if you open a .java file on Eclipse, it should be showing you the updated code that you pulled.