There is no need to worry about lost link juice for internal links. You "lose" link juice when you use nofollow or when you link to something in robots.txt. Many sites do one or the other of those with a large number of links on each page and yet they continue to rank just fine.
I've experimented with this before. I've tried to hide links from Googlebot so that Googlebot conserves every ounce of Pagerank. It doesn't help.
My theory is that Google uses internal links to assign a weight to each of your pages and then scales those weights by your domain rank. "Losing" internal Pagerank ends up not mattering because of that scaling factor.
Writing links with JavaScript won't even help these days. Googlebot does a great job of parsing JavaScript and can render pages just like a real browser does. Googlebot would be able to see any links created by JavaScript just as well as normal HTML links.