Since I was "raised on" R1 subs and only later moved on to fansubs, I don't really care if honorifics are included or not. I don't mind them being included. However, they can lead to secondary problems like overly-small text, too much text on the screen (2 lines spanning the whole width of the image = bad, 3-liners = worse), or oversimplification of the main content. If they're not included, I can hear them in the audio just fine.
And that's one of the main arguments against them -- they don't provide useful information to people who don't already know what they mean and how they work. Whereas people with enough Japanese knowledge to understand honorifics can parse them out from the audio. Do any modern fansubs have
info like this in-episode or on their forums? No, they expect people to already know it all, which creates a steep learning curve and thus a barrier to entry.
Buuuut... I'll turn around and say that I'm guilty of the same behavior in the fansubs I work on. I use the standard chan/san/kun/sama suffixes, as well as standalones like senpai and sensei. Sibling terms get translated though, as addressing elder sibling by title is an uncommon but not unknown practice in English. If I do keep onee-chan and the like in, I restrict them to direct address only. Indirect references get replaced with "my <sibling>", <name>, or other alternatives.
After all, my goal in fansubbing is to maximize praise and minimize criticism while maintaining my vision on how to present the anime in question. On the honorifics issue, you have A: {People who want honorifics}, B: {People who don't want honorifics}, and C: {People who don't care either way}. Since A are more numerous and outspoken about their preferences than B, and C won't complain either way, it makes more sense to include honorifics in fansubs. Not so much on DVD subs, due to the "barriers to entry" problems.