Yeah, I usually don't keep honorifics. The only one I keep is "-senpai", because it's a cultural/technical term that is significant but not really translatable. But if this was a professional translation I'm not sure I would keep it either.
Ugh. Honorifics contain so much context that when they are missing it feels like you are missing half the story. And there is just no good direct translation for them in English, where he have no clear way to denote (or desire to denote) fifteen different levels of respect, deference, or familiarity--and that's just when talking to a sibling!
To me, stripping out the honorifics also strips out a good deal of the Japanese culture that informs and colors the storylines. And if you are stripping out the Japanese culture in manga, then you are doing little more than reading American comic books, except that everyone has eyes the size of tea saucers. You might as well change all the octopus and rice in the dinners to hot dogs and mashed potatoes while you are at it.
I'm not sure why non-professional translators would want to strip out honorifics in the first place. 99.9% of the readers of fan-translated manga are people who are already well versed in the ins-and-outs of -sensei, -dono, and oujo-sama. The other 0.1% are people who are reading their first manga, and are going to find many more challenges from the culture shock than just the nuances of honorifics.