If you look at that investigation objectively, Hillary broke the law by having a goddamn server in her house, which later resulted in a felon and sexual offender having access to classified information.
They could have certainly charged and convicted her, but it would cause disruption in election process and all kinds of crises, akin to what can happen if they go after Trump. This isn't 1970's and the crimes they're being investigated for are technical offenses in nature. Leaders rarely get prosecuted for those crime. I don't like it either, but that's the reality.