Should I host articles on shopping cart CMS, or on a blog?

So, I am trying to move my articles from my shopping cart, which are now hosted as CMS pages, to a blog which I have setup at blog.mysite.ex.

In my blog, I have plenty of articles that say, want to buy "this" or "that" and they point the visitor to mysite.ex/this.html or mysite.ex/that.html.

When the articles were posted to my store, the internal links were all, "/this.html" and "/that.html" . Now I have to write out the entire url. Will Google see that as a ton of external links going to the same site (isn't that abusive?) or is Google smart enough to know that blog.mysite.ex and mysite.ex are the same company?

I had a SEO firm awhile back, look at another blog of mine which had like 200+ links to one domain, while other domains had just a fraction of the same link count to their domains. He said that was bad. It will happen if I set up blog.mysite.ex like this.

I could just keep the articles hosted on the shopping cart CMS pages with internal links like "/whatever.html" but I feel like Wordpress would be more SEO friendly with that sort of content because of articles, tags, feeds, etc.

Please give me your feedback.


Mod's note: Changed original title for this thread, which was:
Does too many external links, to your own site, hurt a blog?

[edited by: Robert_Charlton at 3:17 pm (utc) on Oct 4, 2014]