The 90’s have a lot to answer for when it comes to comics. One of the offenses committed then was the overabuse of thought bubbles. Thought bubbles had been slowly drifting into disfavor for decades, but after the 90s, thought bubbles became nearly taboo in the comics industry.
A major part of the problem was misuse of thought bubbles. They were used as exposition devices more often than not. Comics are one of the best places to show instead of tell, so characters explaining things to themselves that they already knew in their own thought bubbles gets annoying fast. It’s not as bad as the old “as you know” exposition, but it isn’t far off.
The loss of thought bubbles is just one of the many parts of the backlash against 90s comics, but it has survived some places, notably in Deadpool. The primary reason for their success there is the conversational tone they take. Batman and the Bat-Family also get away with it, usually through using thought bubbles to plan actions. (I should note that I differentiate between protagonists narrating a comic in their head and thought bubbles, they’re very different things in my book). So there are ways to do them well, and some comics have kept them alive. (Almost universally as rectangles, though).
And do you know what? I’m totally in favor of bringing them back more often- in the right scenarios. Just keep exposition in thought bubbles to a bare minimum.