I do it in my comics. I keep my casts pretty tight and each character has a unique color associated with them for character design purposes, so the speech bubble is typically a pastel version of "their" color (with the exception of one character who is kind of a jerk, so she gets a dark red bubble with white text). I also plan the layouts and speaking mannerisms where the bubble color isn't necessary to tell the speakers apart, but I think it's kind of silly not to use something that's available to you. Like if it stylistically doesn't fit your comic, then that's cool, but there's nothing wrong with trying to add as much clarity as possible.
I don't think the color matters so much as consistency. Like if your bubbles change color with emotion, don't suddenly color it for normal character speech, or vice-versa. I kinda messed-up with that in Engram where I kept fooling around with the colors to make them more aesthetically-pleasing and it's not a good result, so I established clear rules when I started working on the next project.
