I haven't produced a clutch of my own yet, so really I'm just spitballing here, but it seems to be that candling is a totally non-invasive way to ensure that you aren't letting your female incubate infertile eggs for 60 days and probably refusing food for that time. Also, and again, not based on personal experience, it seems like infertile eggs or ones that start out fertile and fail to develop are the more likely ones to grow mold or start to go sour and could possibly affect your healthy eggs.
Just what I've gathered from reading around this forum and watching the boyfriend with his corn snake eggs, which he does not cut btw. If all the eggs in a clutch have pipped except a couple, he'll try to wait them out and if they haven't pipped within a day or so he'll cut to check on the baby but it seems like those end up containing dead-in-egg babies most of the time anyway.