Placing the navigation bar in the html code not near the head, or even on the bottom to favor the contents (the users would view the menu as a topbar using flexbox source ordering), can improove SEO? Considering that Google Sitelinks are based on the navigation structure, could the same navigation structure be a discriminant to get them?
The placement of the nav bar has no effect on SEO.
According to John Mueller, Google's Senior Webmaster Trends Analyst, the positioning of internal links on a website do not impact the site's SEO:
Position on a page for internal links is pretty much irrelevant from our point of view. We crawl, we use these mostly for crawling within a website, for understanding the context of individual pages within a website. So if it is in the header or the footer or within the primary content, it’s totally more up to you than anything SEO wise that I would worry about.