Weebly wasn't initially designed as an ecommerce platform such as Shopify which is specifically for ecommerce, so you'll always encounter some type of design flaw. But in my experience, Weebly really does listen to its users and work to provide solutions to your problems. 

As for your SEO issue, it's quite simple. There are TWO boxes you must click to hide things from all users and also hide it from search engines. Clicking the button below hides the page from being navigated via the Nav Bar:

Keep in mind, if this is the only box you click, the Page wont appear in your Navigation bar once Published, but it will still be crawled by Google and picked up as a page, since the page is still technically published. This is useful if you create specific Landing Pages for ads and want them to be indexed and boost your SEO due to the views they receive, but you don't want the landing pages in normal navigation.

Click SEO Settings on the page you want to hide. 
Scroll to the bottom and click the button shown below as well:

The second button is actually Weebly providing Editors the ability to click and input Robot.txt onto the page so it doesn't appear in SERPs. Click those two buttons and the Page will (once SEO kicks in) not appear in your Nav Bar nor in SERPs.

Hope that helps!