Question: It's a common practice to highlight an element on hover state. 
By highlighting it, I obviously mean making it more visible than other elements.

But lately, I've witnessed the opposite trend on a couple of websites : 
Opacity is set to 0.5 or less on hover, which makes the hovered element less visible instead.

To me, this is nothing but a bad practice.

Or is it a new trend backed by some well known data that I'm unaware of?

Answer: 
I see your point – but I'll try to explain in two paragraphs why I think it's **not** 'bad practice' at all, while personally I also dislike this effect.

* Trying to imaging the opposite approach: every element has an oppacity <1 and only the 'highlighted' element has an oppacity =1 does not feel 'right' or 'better'
* 'highlight' in the context of a group of objects doesn't automatically mean, that the object/image should be seen 'as it should be' or 'with full saturation' or 'brighter' or the like. It basically only means the highlighted object should '***stand out***' from the rest. How that '*standing out*' effect is actually achieved is a different question – e.g. thinking of this text-overlay-effect that is/was quite popular, or changing color in text-links, or adding a border or the like – even making an object invisible on rollover. All of these practices could be technically considered 'highlights'.

One more 'real world' example: in the top navigation here on ux.stackexchange.com the main menu items ("Questions", "Tags" etc) change color on rollover – from bright white to some yellow/orange tone. So technically the rollover text's contrast to the background is lowered on hover. But IMHO it's still a '*highlight*' effect since it gives you a visual feedback that your mouse pointer is within the linked element. The menu item stands out from the rest – it's highlighted.
I agree that it is **currently** a bad practice, primarily because it is returning to the days of metaphoric design. The designer is trying to inspire the appearance of (and a realworld reference to) a frosted sheet of glass floating above the surface of the rest of the interface.

In this age of Modern-UI, it is common practice to avoid metaphoric/skeuomorphic elements in our designs.

From a purely UI standpoint, I don't think there is anything wrong with floating sheets of frosted glass. They are pretty in a nostogic kind of way... and they do focus the user's attention on a subset of input options which is what they are supposed to do. 

They just are currently not popular; non-standard enough to be considered mainstream yet still too familiar to called revolutionary. Just a little too... dated.