ESN doesn't use 'their' software so much as you just put the cd in, hit a few keys, it remembers it, and you then put THAT cd away in a safety deposit box.
I can't tell you how many people would come in with their radios, putting them in new cars, only to find that the cd they used to program the ESN was missing, had been broken, etc.
As for hiding it, other than fabricating something, it's a risk you just have to take when getting into car audio.
Tinting your windows will only do so much. You can still see in there.
Not booming your system when pulling into parking lots is one thing you can do to protect your investment.
Also, watching where you park as well.
Just about everyone gets hit at least once in their life, it's just something you have to be willing to deal with if you go this route.