You can also play in E Dorian over this, it won't clash with either chord (E minor consists of 1-3-5th degrees and D major of 7-2-4 degrees of the scale - neither chord has the sixth degree in it)
Technically, the correct numeric label for this progression is: i - bVII The numbers that you wrote, in the key of E minor, would yield the following chords: Em - D# D is the b7 of E.
You know whats interesting - I've seen in both ways. I've always learned that you treat the natural minor scale like the standard for roman numerals in a minor key and the Major scale for the numerals in a major key. That way writing a progression like Em D C as "i VII VI" indicates that I'm in natural minor whereas writing a progression Em D#° C as i #VII° C would indicate harmonic minor progression. Doing it your way would put the first progression as "i bVII bVI" which is comparing to a major scale. If there is ambiguity out there, I'm going to stick with the way that reflects the theory more clearly.
