Is search engine optimization on a mean.js full stack javascript application still a major issue an how should it be dealt with

If you are rendering the majority of your content using a JavaScript, then yes, it becomes a search engine black hole. That's one of the big downsides of a thick client application. If you need high visibility by search engines, it's a challenge. There is a middle ground.

You'll need a combination of server side rendering and client side rendering. When the page first loads, it should have all the visible content the user needs, or at least the content that appears "above the fold" (at the top of the page). Links should be descriptive and allow search engines to dive deeper into the site. Your site's main menu should be delivered with the web page as well giving search engines something to bite into.

Content below the fold, or paginated content can be pulled in dynamically and rendered on the client using any JavaScript framework. This gives you a good mix of server side rendering to feed search engines, and the performance boost that pulling content in dynamically can offer.

well you'll need to be worried about the public face of your site you shouldn't be considered anything behind a log-in screen, to me the snapshot with a headless browser approach using the farment_scape seems is the way to go, it's the one that will consume less time and as you looked at mean-seo isn't that hard to implement.

take a look to this question, there are some answers about how to creates links on the pages to be SEO friendly, almost all the recent posts fit together one to each other.

https://support.google.com/webmasters/answer/174992?hl=en

and also try to register to https://webmasters.stackexchange.com/ you'll find more about seo

Just wanted to mention this npm package https://www.npmjs.com/package/mean-seo which uses PhantomJS to render a preview of your app and caches it on the disk/redis for whatever period you set.