I use middle mouse click, thumb mouse click, control click, and right mouse click + left click on "open in new tab".
Each method is dependent upon various things including, how I'm sitting, number of items I plan to open, number of comment sections vs just article link, and most importantly, how sore my hands are. Some methods are faster but strain my wrist more than I care to do, so I do those sparingly.
One of the reasons I love this site is the UI, it's very simple and gets out of the way for you. If you want to change the opening mechanism to only do new tabs, you are completely able to do so with code.
To answer your question, there are a variety of reasons why HN may choose to do it this way, other sites have different reasons so you see different site behavior.