Let's put it this way....1. Google expects to see pages like FAQs, About Us, Contact Pages, etc have a high number of internal links.
2. The link equity "leaked" to these pages is usually negligible. Sure, there's a small amount of PageRank, but it's not really considered anything that would influence your on-page optimization.
On the other hand, if the links were in obvious places, and there were a lot of them, I might be tempted to control my link equity as well. It really all depends on where the links are placed and how prominent they are on the page. "How likely is the user to click this link?" is a good question to ask a.k.a. "reasonable surfer"
3. At the same time, Google probably doesn't care too much that you removed those links, either. Very rare that removing links is seen as over-optimization.
4. Google is getting very good at following javascript links. They many not show up in Google Webmaster Tools, but it's likely they are parsing your javascript anyway. (unsure how much link equity, if any, flows through this)
If you're concerned about it, you can simply watch your rankings, traffic, and crawl stats to monitor for problems. If there is, simply revert your actions back to the original, and hopefully everything will be good.
Best of luck with your SEO!