I don't know about EverNote but I tried to develop a personal wiki under iPhone more than two years ago (not with markups but with a "rich" editor).

Finally I desisted because [technical rant] While I can use the UITextView (an UIWebView) there was a big possibility to be refused on the App Store after using some hidden methods. The other alternative was building a complete rich editor myself but was outside the project budget.

So, I believe that EverNote must follow a similar route to include links and others features.