Justification is not readily supported for ePub as of yet. With CSS it can be set without much trouble, but the readers will not support it yet.
I believe there is a whole discussion about what is better, justification or left alignment. Personally I would very much like justification support in readers soon. For Sony readers the technology is present, because Sony's own format can be justified. My feeling is that it should not be a big deal to implement, but apparently it is.