Custom build sites for an Online Shop look more professional than WP themes. WO is easy to manage, so one may consider it if (s)he is not a techy person to maintain a custom site.
We provide WordPress ecommerce solutions. While it "appears" to have a lot of functionality, it is really for very small shops and ideal for small numbers of products with limited variations. It is ideal for companies that might sell tickets, a service, or a few products. It is not meant to do thousands of transacations. www.activewebgroup.com/wordpress-ecommerce
Yes, you can use Ecommerce with wrodpress CMS. You can find lot of plugins for that. I recommend to use WP Shope plugin for ecommerce website.