I like Jude and Ruby better then Elias and Ruby. In terms of working I think the really depends one how much you want your children's names to line up and how important that is to you. I mean there is nothing to stop you from having Elias and Ruby but I would think Elliot and Ruby work better together. And with Elias, Ruby and Jude then Ruby does stand out. But it might not be something that would really bother her.
It depends on whether or not it bothers you. Most people in real life don't overanalyze sibset names. I see that Elias and Jude go together, and Ruby and Jude is a bit better than Ruby and Elias. But at the same time, if I knew a family with these names, I'd probably just think the kids had cool names. :)
I don't see any issue, unless its two of the names being Biblical or two having U's. I don't care for Elias at all, but see no real issue with those three names together.
I like all three together.