This is an issue with Japanese scripts, and you're right to be annoyed by it.
My personal rule of thumb is to replace ellipses with periods
. THEN add them back in if appropriate
Grammar Girl summarizes, "... use ellipses sparingly to indicate hesitation or faltering speech or thoughts, and use them to shorten long quotations when necessary, but be sure you don’t change the meaning."http://www.quickanddirtytips.com/education/grammar/ellipses?page=2
She recognizes that they do get used in unconventional ways in comic strips, "... Charles Schulz always used ellipses instead of periods at the end of sentences in Peanuts."
I'd encourage you to do your own research. I was recently recommended The Chicago Manual of Style by D (remember him?). You may want to consider keeping a copy of that around.
As for an abundance of "what/huh", the same "less is more" rule applies. Don't be afraid to omit ones that are unnecessary.