safari to open external links in new window
I've experienced the same thing, new windows instead of tabs opening when control clicking, and it has seemed totally random to me, too. 

The Safari Extension 'Link Thing' (maybe 'LinkThing' -?) will, by default, open all links in a new tab without your having to hit control unless the page (e.g. DuckDuckGo) disables and overrides the user's browser preferences.