Does too many links in the main menu which is the homepage going to hurt my rankings? As an eCommerce site I have plenty of links and many of the on-page SEO checking tool are suggesting that is bad for rankings.
If they are linking to real products then it won't really matter how many links do you have. You said you are using tool to determine them actually. Tools are build for normal site such as blogs, company site etc so they will tell its bad indeed. Think of amazon they have plenty of products in the homepage that doesn't hurt them so why should you will get hurt.
It really depends, I mean its an e-commerce site and usually this type of website has a lot on links incorporated with it.