The problem is that most developers created their iOS apps in the expectation that they would only run on iOS. So, for example, paid app developers who were willing to live with a small # of users pirating their apps on jailbroken devices might not have bothered putting in code to verify receipts or otherwise guard against piracy, and likewise developers of free-with-IAP apps might have left those systems trivially easy to hack (say, editing a preferences file) expecting that people would only be able to hack them if they jailbroke their phones.
Likewise, many developers - including myself! - have signed copyright licenses that specify that a piece of content is licensed for use on a particular set of platforms / form factors, a set which might not include Macs. So if our app had turned out to be able to run paid add-ons on Mac, we would have been violating our license agreements with those publishers through absolutely no fault of our own. (and would have probably had to take much more severe measures to prevent use on Mac in that case)
There's also the business model end of it. Say that you built a beautiful Mac-native version of your app that you charge $50 for, and then a beautiful iPad-native version of it that you charge $10 for. Those prices were perfectly reasonable given the number of users you expected each version to have, but now that Mac version you worked so hard on suddenly seems extremely overpriced because people can just buy your $10 iPad app and run that on their Mac, even if it doesn't work as well. There are other variations on this too, of course - it could even be that the Mac and iPad apps were more-or-less functionally identical, but this particular app happens to be much more useful on Mac than on iOS as a form factor, and so they were selling the iPad app as a companion of sorts, with the Mac version underwriting most of the cost.
You can argue that that that was a bad / unfair business model and that the developer should have been charging the same price for both apps from the beginning, but as of a year ago this was still a perfectly sensible thing for them to have done, and now their business is getting blown up just because Apple couldn't be bothered to apply even rudimentary copy protection to iOS apps on Mac. Moreover, Apple didn't even warn us that this particular problem was coming - they sent a couple of emails telling us to opt out of Mac App Store distribution if we didn't want our apps on iOS, but there was nothing about needing to add code to your app to detect that it's running on Mac and throw out an error / crash immediately / etc if we wanted to actually make sure our app couldn't run on Mac.
I don't agree with the idea of requiring all Mac software in general to be signed, but I do think that apps that were signed for / distributed through the iOS App Store should not be runnable on Mac without the developer's consent, and I support whatever technological measures are necessary to make that the case - it could be as simple as automatically blacklisting any App Store app that had not opted into Mac distribution, but they need to at least do *something*.
The part of your argument I unreservedly agree with is that Apple should've given fair warning and the how-to for developers to make changes on their side ensuring their apps would not work on Macs if they did not wish so, giving them a chance to push updates BEFORE Macs with ARM became available. This way they could've better protected developers' IP and their business models. Now it will all have to be done in a rush.
On the licensing issue though, I think this is no different from Android apps running on emulators. You made an app for iOS (and Android), and you don't officially support it on other platforms. People who find a roundabout way to run it on other platforms can't complain if something is broken or come to you for assistance. Perhaps you're expected to take "reasonable" preventive measures, but you can't cover for every possible hack/workaroud. You can start implementing the necessary changes now that you're aware of the issue.
I'm against irremovable locks to the OS though, as I think this is a slippery slope. I'm not very optimistic on Apple keeping MacOS open for the long-run though. I believe that in the end people who really want to be the actual owners of their computers will have to run Linux or some other open-source OS. But I don't want an IP-protection issue like this one to be the trigger of the Mac's downfall.