Chuee

The only reason to leave them in is because taking them out makes certain situations an absolute pain in the ass. For example, when characters specifically mention the honorific, or go from calling someone A-san to just A, or A-kun/A-chan. For example, one scene in the game I'm editing has the main character meet a heroine for the first time, and the dialogue goes something like,
"Okay, Mizunose." 
"...No honorific?"
"Ah, sorry. I'm not really good with these things."
If you were to take out honorifics, you'd basically be forced to rewrite the entire dialogue here.
I'm sure people that translate literature more than likely just cut things like that out, as they probably do with every "Itadakimasu.", because they can. Though translations of things like VNs and anime are less at liberty with what they can and can't do, so it's more easier to just leave them in and expect the reader to understand them decently enough (which the vast majority of these people do). 
 

What kind of fan-translations are you playing? At least from what I've played, most have glaring mistakes. This game read 10x better than most fan-translations I've read. The only problems being the translation choice that's currently driving you insane, some wording choices I felt were wrong, and the few translation errors I caught. The norm for fan-translations is stuff done by Ixrec or TakuJun which read stilted as ever-living hell. If you think this is a horrible translation I'm not sure you could read through something like Fate/Stay Night and actually survive. 
 
 

I'd much rather take that than having to reword sentences constantly in my head while reading something or having to deal with transliterating dots (god this annoys me so damn much now). I've had problems with the way certain words or phrases were translated in official translations, even phrases that were reoccurring. Though maybe I just didn't care that much about the tricky use of tricky because I lost interest in this game after like an hour in the first route. Oh well.  

Not really. The average fan-translation is garbage, and I'd say this was a lot better. Far from perfect, but you should probably stop getting so incredibly anal over a single word. 

H-Scenes are tons of fun. Especially when the word penis is never used, and genitals are always referred to with non-decent sounding words. Then add on all the terribly strange sounding lines that make you cringe. Something like "The joy of being born a woman" or something? That one was nice.