This is not an option with Square, However, if you don't use your online store for consumers then you could hide it behind a login page on your website. The Square store is not searchable if you don't have a custom URL pointed to it. (Anyone can still order form it if they have the stores URL.).
If you have a consumer site you could create a second location just for wholesale and do the same thing. This time however you have a public site and a hidden site.
If this doesn't work you may see if one of the e-commerce apps have this capability.
