Most comic lettering fonts are all caps because that's how the hand letterers did it in the pre-digital age. It's since become a natural part of the "comic book look." People simply expect the dialogs in a comic to be lettered that way.
That doesn't mean you can't use lowercase fonts. There are a few cases, like
Soil, where the relatively small speech bubbles and "rigid" artwork might be better served by such a font.
You could also combine both type of fonts by using the lowercase font for whispering and non-verbal vocalizations like "uh," "heh," "umm," etc. It makes the dialogs livelier and more fun to read.
I'd like to think that choosing a font for a manga is more than just a question of taste/preference. A good letterer chooses fonts that suit the manga's artwork and don't distract the reader too much. Make no mistake, bad font choices are more likely to ruin the reading experience than a bad translation.
For more information on this topic, I strongly recommend
this guide by Nate Piekos (of Blambot fame). Every typesetter who takes his/her job seriously should at least be familiar with the rules and conventions described here.