I'm pretty sure you with HTML5 you can have one

per container element. Therefore, while having the logo as the

isn't ideal, it won't hurt.

I have heard a lot about having a solid internal linking structure so that Google can easily discover pages and understand your page hierarchies and correlations and equity can be passed. Often, it's mentioned that it's good to have optimized anchor text, but not too optimized.

You hear a lot of warnings about how over-optimization can be perceived as spammy: https://neilpatel.com/blog/avoid-over-optimizing/

But you also see posts and news like this saying that the internal link over-optimization warnings are unfounded or outdated:
https://www.seroundtable.com/google-no-internal-linking-overoptimization-penalty-27092.html So what's the tea? Is internal linking overoptimization a myth? If it's true, what's the tipping point? Does it have to be super invasive and keyword stuffy to negatively impact rankings? Or does simple light optimization of internal links on every page trigger this?

If a website doesn't have a true folder structure, how much does have the page path structured like 
/shoes/rain-boots/ actually help establish hierarchy and flow of equity?
Since /rain-boots/ doesn't actually live in the /shoes/ folder?

Will you simply have to use internal linking to get the same effect for the search engine?