Now that I've read several more books on my Paperwhite, I have definitely noticed what you are talking about. Because I keep the font on size 2, it isn't often that a long word breaks up the justification, so I didn't notice it at first. However, just to weigh in again... Hopefully I don't offend you like I've obviously already done from the tone of your response.
I have a hypothesis for why Kindles might do this. Before I switched to a Paperwhite, I owned a Nook Simple Touch and a Nook Simple Touch with Glowlight. These e-readers did have hyphenation to allow for unbroken full justification. You know what I noticed? On those words that were broken with hyphenation, you could never use the extra features on the menu you get from touching the word like looking up definitions, etc. Perhaps Kindle had the same problem, couldn't fix it either, and instead of leaving the features broken on these words, decided to solve the problem by preventing the situation from happening in the first place.
Again, just my opinion. Sorry for offending.