How do you confirm Google read Javascript and how did you check that? just curious
In webmaster tools I set up 5 different sites that I owned (for testing purposes) . If you don't own that many sites like me, just "Sub-domain the sites you have" and set those up in Google Webmaster tools.
Then link one of the sites, I call this Site A to Site B, Site C, Site D, Site E via Javascript using different methods. Then wait a few weeks and check the "Linked Domains" on site B-E in GWT (You will see site A on the list)
I don't really what you are saying to. Can you explain in more details for this?
The page that's normally linked the most of any website is the "Homepage" - It's not secondary pages. You're company lets say has 1000 incoming links, now your homepage has a lot of ranking power, so it uses that power and passes the link juice to all the other pages on your site that it links to. If you have a link to a "Terms of Use", a "Privacy Policy", a "Contact Us" it funnels ranking power to those useless pages, they are not your money pages. Why give them link juice? Removing the links from your home page allows the more important pages to rank better, but it's not customer friendly. Javascript linking to them could of been a solution and was a solution in the past, but it's not anymore. So the only thing left is a "Server Side" re-direct.
Read up on page sculpting, here's an article from Matt Cutts.
[URLnofo]https://www.mattcutts.com/blog/pagerank-sculpting/[/URLnofo]
It's does not violate any terms of Google SEO, it's not considered Blackhat. You're just controlling how you want page rank (link juice) to flow.