In the following, when talking about displaying a presentation with a certain aspect ratio on a projector with a certain aspect ratio, I always assume that the presentation’s aspect ratio is preserved and black bars are added at the appropriate sides. Never have the projector digitally warp your presentation: It destroys hinting¹ and may make fine lines invisible.
The best aspect ratio is the one of the very projector you are presenting on, as you can make best use of the space. In particular with projectors, you do not want any content to be unnecessarily downscaled as their resolution is very low to begin with and the projection area may be rather small (and thus difficult to see for the audience). An okay 16:9 presentation may be rendered unreadably small, if displayed on a 4:3 projector.
Now, depending on your presentation and how dynamical you program it, adapting to a different solution may be a rather simple thing with Beamer (apparently in contrast to Powerpoint, going by the article you linked). I once changed a presentation of mine from 4:3 to 16:9 in about half an hour, and this included recompiling complex animations and a lot of perfectionism – a “normal” presentation could be adapted much faster.
If you do not want to adapt, the choice essentially depends on the average age and purpose of projectors in your conference venues (I would guess that newer projectors or projectors mainly used for movies are rather 16:9). Thus it depends on your field and probably also your continent. Anyway, most projectors I have encountered so far had a 4:3 resolution and most of those who hadn’t had a resolution very close to it. I’ve only encountered a single 16:9 projector. I thus use 4:3 as the default.
¹ To give you an idea, the following shows this sentence as natively rendered by my computer (with hinting) and the same text digitally stretched or squeezed: