Nope, you're confused here. E is never = Eb. That would be like saying 4 = 3. A pitch is a musical frequency. It is essentially independent of the physical means used to produce it. An E is not defined as the open lowest string of a 4-string bass. It is defined as ~41 Hz (qualifier: in current Western common practice). If that's the note your lowest string is tuned to, then playing that string open will produce an E, but if you tune the string lower, it's not an E when open any more. This is obvious when you detune one string, as when you play in drop D; it should be equally obvious when you detune all of them.