When checking references for a job applicant, employers may be reluctant or prohibited from saying anything negative, so leave or send a message that says, “Get back to me if you highly recommend this applicant as super great.” If they don’t reply take that as a negative.
When you flush a candidate on a reference check, there's a good chance that he'll figure out what happened, and justifiably become paranoid. He's going to assume someone deliberately ratfucked him, which is not necessarily what happened here--the person could have legitimately thought highly of the candidate, but forgotten to reply because the email came at an inconvenient time (or ended up in the spam folder). At the minimum, you're destroying someone's professional relationships, but if this is in an industry like Silicon Valley, where people have glowing references not because of sincerity but because everyone who matters retains a hit man to "fix" negative ones, you're putting people in danger of physical harm, including the possibility of death. Worst of all, since the candidate might not know which reference ratfucked him, you could end up getting someone innocent killed.
So, don't do this. The main function of reference checks is to ensure you're not getting someone who claims to have worked at Goldman Sachs or Google for 4 years but actually never set foot there. Leave it at that and be happy.