To be blunt, you do not have to create a developer account, sign binaries, or share 30% of your revenue with Microsoft. MS's API are not a mess in my opinion. You do have several options (traditional Win32, .NET, UWP, etc.). These options all work fairly well and are very flexible.
As for, Apple, I do not know but I suspect you can make Mac applications without a developer account. You need a developer account for iPhone. It's $99 a year the last time I looked. This is not a lot of money if you are serious about making an application.
If you don't sign your Windows installer, then the first N users to use it will get a scary pop-up message saying that the AV "protected your PC." I think you might also need do code-signing if you distribute through the MS store.
Compare with the web where LetsEncrypt just works without demanding a king's ransom.
As for the APIs, it is very easy to get into dependency hell between all the different UI technologies, .NET implementations, and target systems. Want to develop a brand new plain-old GUI app? Probably simple (although I've never tried, the web is right there). Need to develop a plugin for an existing application, or a new app for something like Hololens? Have fun.
It's a bit worse with windows. You can get a scary warning or you can get smartscreened to death and the app will be prevented from starting. This is random / depending on functionality and effectively impossible to test with 100% certainty.
As for, Apple, I do not know but I suspect you can make Mac applications without a developer account. You need a developer account for iPhone. It's $99 a year the last time I looked. This is not a lot of money if you are serious about making an application.