If a site doesn't validate, it might not appear properly in some browsers, reducing your customers' experience of your site. In extreme cases, it might also mean that they can't (eg.) see your buy button, killing your sales.
Major e-commerce sites will have tested under every major browser anyway, so invalid HTML won't matter so much to them. Smaller shops don't tend to do as much testing, so it's more important that HTML validates.
If it doesn't, it's probably rendering in quirks mode, and you'll have all sorts of problems with the layout if you need to change it.