If you connect to a jira instance through https and use a proxy like webscarab, you can decrypt the conversation without warning from the plugin.
Checked that other applications detected the wrong certificates.
Product Version: NetBeans IDE 7.0.1 (Build 201107282000)
Product Version: NetBeans IDE 7.1 (Build 201112071828)
Product Version: NetBeans IDE Dev (Build 201201260600)
Java: 1.6.0_20; Java HotSpot(TM) Client VM 16.3-b01
System: Linux version 2.6.38-13-generic running on i386; UTF-8; en_US (nb)
I don't know for how long I will have access to a jira environment to reproduce this behavior, please evaluate it and give some feedback like an estimated release date.