You are completely correct. No software only security mechanism, least of all one from Apple, has stood the test of time.
Hacking SIMs is not impossible, but the amount of effort and the cost of the equipment needed to do so almost certainly isn't worth it. No point spending £ks+ just to hack someone else's SIM so that you can get a few free calls against their account. That's why it hasn't happened.
But if the effort were suddenly no harder than downloading some clever app, every nefariously minded person out there will be able to do it at no cost. So it will happen a lot.
So will a network go along with this? It's a mighty big gamble. In effect they will be placing the security of their billing and revenue systems in the hands of someone else like Apple. Apple get that wrong, O2 (or whoever) and their customers will lose out. Where is the commercial incentive for Apple or any other manufacturer to get it right? Almost entirely non-existent.
And what happens if your phone goes flat, breaks or crashes? Apple phones have not exactly been famously immune from such problems, nor has Android, Symbian, or anything else. So when your phone stops working, how do you get your standby emergency old handset going with your phone number? At the moment you just put the SIM in and off you go. But with a software SIM, no doubt heavily locked away and not easily accessed at the best of times, you won't be able to do that.