It really only inactivates it, and you need to make sure you set it to "Custom" as well, otherwise any updates to those scripts will cause your change to be overwritten.
By setting it to deleted future scans shouldn't find the vulnerability anymore (shouldn't even be an option in the scan), but the Asset Reports will still show it from previous scans, and there's no way to "remediate" them if the scripts *deleted* i.e. future scans can't determine if the issue still exists and will not negate the previous findings.
To keep from getting flooded with Informational results you could always create some Vulnerability Sets, and scan for and report on only those Vuln Sets?
I hope that helps!