Hi,
These are indeed good questions.
1. Regarding the 404 URLs, if your screenshot is from weeks ago, then no wonder that it doesn't match with what I can see on your website. Unfortunately, I can't say much in that case. I would need a recent report on issues, to be able to say what to do.
2. Regarding the canonical URL, it's a double edge sword:
- if your products' details page can be accessed with different URLs, you want to enter the main URL of the product in there. That way, you'll be able to guarantee that this will be the URL used for the indexing of search engines. Also, if search engines find other URLs for the page, they won't penalize your website for it. So having a canonical URL for each product is what I would recommend for better SEO.
- Now, having a canonical URL for a product means that this will be the URL used. Suppose you enter the URL
www.hikashop.com/extensions/hika-essential.html
for the product "HikaShop Essential". Then, two years later, you decide to change the alias of the menu item "extensions" via the joomla menu manager to have instead "our-extensions". This is fine, but you need to also update the canonical URLs of your products. If you don't, the links to your products will generate 404 errors because there will still be "extensions" instead of "our-extensions" in the canonical URLs. This will downgrade your pagerank, so you want to avoid this situation from occurring. If you think you (or the webmaster of the website) will want to change the structure of the menu items, and can't (or will forget to) update the canonical URLs accordingly, then leaving the canonical URLs blank is better overall.
3. It depends what you have in it. I can't check what you have in it unless you provide a copy of its content, so at the moment I can't say. If it's a mess in there, then you might want to start from scratch with the default Joomla htaccess.
Ideally, I would recommend being as close to what Joomla has by default as possible. This will simplify maintenance in the long run and will prevent issues with SEO when things change around.
But some things can be nice to have in it. Like for example automatically redirecting from http to https.