What am I doing to scare away prospective PhD students?
I am not a prospective PhD student but a current one, and I am not in the mind of every PhD applicant, but my best guess is that some are not really interested in your department, some don't know how to say "I actually accepted an offer at a different school" with good manners, some are not fully sure if the e-mails come from a human or from an automated system (especially those who come from countries with a strong culture of professors ignoring or being mean to students, especially undergraduate - I wouldn't have imagined I'd receive personalized e-mails either!), and some are just rude. Or maybe it's just generational: in the same way it's starting to be considered more polite to never reply a text again than to politely decline a second date, and that many prospective employers say "we'll call you" after a job interview and they never ever call, there might be some perception among some people that it's better to be silent than to reply negatively? I don't know. Do they get interviewed before receiving an admission offer? Are they aware of how many offers you make out of a larger applicant pool? Emphasizing that might entice some of them to continue the conversation, or at least it might dissipate the question on whether they were not aware of things or, instead, they were plainly impolite.