Hi Pavel,
I'll let someone else speak to whether native shadow DOM will be the default in 1.0. I think the reason shady is the default in 0.9 is that it's helpful for testing (both testing the shady DOM code, and ensuring that people get styling that's more consistent with what they'll see on browsers that don't implement shadow DOM natively).
With 0.5, we saw a lot of people develop on Chrome, and get taken by surprise by styling changes when they tested on another platform.
That said, if you are positive that all of your users are on a browser with native shadow DOM, I'd recommend using native shadow DOM. In my experience it's faster and styling is more accurate. You can also avoid using the Polymer.dom() API for manipulating DOM in this case. (Although that makes it hard to switch to shady should you ever need to support non-shadow DOM browsers.)
Hope this helps,
-Arthur