Okay, not sure if this was a bug or a feature, and if a feature, I'm not sure which feature it was.
Had ships in a transport. Had transport cloaked by a cloaker. Had an EMP detonate in system.
IF I recall correctly, the transport and cloaker were both paralyzed and uncloaked (although coulda been a scout that was uncloaked, and cloaker was okay...)
Anyway, transport was definitely blinky red, but to my surprise still able unload units, and to my double surprise, the units were rarin' to go. So my working theory is that you can hide in transports in a pinch to avoid an EMP (I kind of doubt this will ever arise defensively again, but has obvious uses on offense; I'd always waited in a neighboring system when EMPing somebody). So, is this true?