Welcome to the Q&A Forum

You wouldn't necessarily get a "penalty" from the search engines but the pages will eventually disappear from the search results if they are returning 404 response codes, and thus you will lose traffic as a result. Your best bet would be to 301 redirect the inactive pages either to the homepage or to other relevant pages on your site.

I use several tools for rank tracking:

1. CuteRank - Simple and easy to use keyword rank checker and best of all, it's free. http://cuterank.net/

2. Market Samurai - Great software for keyword research and includes a keyword rank checker. http://www.marketsamurai.com/

3. SEMRush.com - I don't really use this site for keeping track of my keyword rankings over time, but it is invaluable for discovering new keyword opportunities since you can see all the keywords your site and your competitors' sites rank for. One way it helped me is that on one of my sites, I discovered that a random PDF was ranking #1 for a popular keyword but since I was only using Google Analytics to track my website visitors, I had no idea the PDF was getting any traffic. So I redirected the PDF to an actual page with the GA tracking code, website navigation and a contact form in order to convert some of those visitors in potential customers.

I am also a big fan of WordPress since it is very easy to use and basically 100% customizable, but in your case, I think you might be better off choosing an ecommerce platform such as Magento. While there are certainly ecommerce plugins for WordPress, I find Magento to be more robust and offer more features for managing inventory, orders, customers, sales reporting, etc. I would also suggest checking out Volusion and BigCommerce.

Also, I'd stay away from Joomla or MODx for an ecommerce site.

90% client work, 10% personal side projects mostly for running my own SEO experiments which may end up helping me with my clients.