I have created a number of PDF books for my PRS using inDesign "automatic" full justification, and the results have always been fine for me. I've also had very few problems with my LRFs.
On the other hand, I purchased my one and only epub on Waterstones, a Terry Pratchett book, and for some reason, the left justification leaves huges swathes of white on the right side. Some pages look as if they're written in verse!
I personnally find it very bothersome. My eyes keep focusing on the hills and valleys the text creates on the right side. I guess I'm just used to p-books being generally fully justified, but it's enough to put me off epubs.
By the way, I'm very surprised at how long it takes Sony and Adobe to remove these kinks. After all, the software is not that complicated and the algorithms have been available for ages. It makes me wonder at the commitment these companies have when it comes to the PRS...