While it's well known in design that lowercase is easier to read.
I think you're confusing legibility with readability. A face can be perfectly legible without being comfortable to read in long passages of text. Most display or decorative faces (assuming they're legible in the first place) fall into that category. A good readable text face like Caslon or Garamond, by contrast, isn't always the best choice for instant legibility (on a billboard, for example).
Handwritten uppercase is more legible in small sizes, especially on newsprint, and the text in talk balloons is usually short. You'll notice that lengthy text in a talk balloon is not so easy to read, but these are very rare.
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A good rule of thumb is not to have more than max 25 words/balloon and 50/panel. Printing sizes of daily newspaper comics have gone way down in the past 100 years, and some are printed on very poor quality paper.