Generally the changes are very small and they don't stand out. I don't have the game up right now as I'm in patch hell, but if I remember right the changes to incinerate from green to blue is it also stuns the enemy while they are burning in the blue, while in the green they can still move around and find you technically.

It depends. From the look of things higher level gear utilises a similar system to when you craft it yourself, so there's a random benefit added which can be anything from a new effect to just increasing the basic stats. Make sure you check them both carefully and that the higher level hack hasn't increased damage or added an additional damage type etc.

With cyber hacks the higher levels seem to either increase the effects (longer time active etc) or add additional effects (spreads to other enemies etc). Sometimes they'll change the basic effect - I switched out a hack which dealt non-lethal electrical damage for it's rare version which now does damage over time.