Redirects usually don't pass all link juice to the target URL but may in time. You won't get accurate reports on the www version of your site because it's redirecting to the non-www URL, so use this primary URL when running reports with SEO tools. Regarding the number of links, you may find that people generally link to the www version just by habit, and that's why I personally still use this as my primary for most projects.
Another thing to do is check Google WMT to make sure both www and non-www properties are listed. You'll then be able to select the preferred domain in site settings.
You didn't ask but I'd strongly suggest you go over some PageSpeed and YSlow recommendation. It's very slow and JS heavy, and this is simply bad for all the reasons you already know.