Lots of questions and comments. It would be nice if someone would fix CPN My guess is there are plenty of people who would pay money for just a one off repair. But I expect CPN is a real piece of spaghetti code. The program apparently dates back to the Next computer, so it's nearly a 30 year old code base!
Aperture seems to work fine in Mojave, along with my 32-bit Nik plugins, but I do have a number of 32-bit programs I use (and for which I expect no updates) so I don't see a way beyond Mojave. I'm still running Sierra on my iMac, mainly because I'm worried about APFS and the Fusion drive, but am running High Sierra on my MBP for which it is the end-of-the-line version. My wife's iMac is running Mojave with no issues but she doesn't have that legacy software problem.
I'm not concerned with iOS compatibility as I don't have an iPad and my iPhone is a "consumption device" except for adding events to the calendar and occasional notes.
Frankly one problem with CPN was that it was a kitchen sink of features. Far more than needed and too many weren't very well polished and keyboard shortcuts were often mystifying so a major learning curve. Growly Notes seems to be solid and is reasonably fast (much improved speed in recent years). It is more free-form like OneNote. Sometimes this is good for organization and other times it just means a messy appearance. Much less hierarchical for organizing than CPN.
There are times when CPN works fine and others where it crashes immediately and this is in contrast with High Sierra where it did not work at all. It is a 64 bit app so that certainly isn't the problem, however, it probably needs some tweaking in the code which alas it will not get. Like many I'm staying pat on Sierra not only for CPN, but for Aperture, Final Cut 7 and some other 32 bit apps. I am using Scrivener as well, along with MacJournal (it continues to work well with apparently no patches or updates but it's UI is cluttered and old fashioned) but nothing really replicates both the easy and the complexity of CPN. Outline from Gorillized can actually import CPN data if you are interested in migrating things forward, but their UI is still not as flexible or as powerful as CPN. I think not being able to create an identical iPad version of Notebook certainly hurt CircusPonies and looking back it's the one piece of software I would have been willing to pay a subscription for. Maybe there is someone, somewhere who can write a patch for this? I have been experimenting with other notebook apps but there is a startling lack of complexity to many as getting the apps to work well for Mac OS and iOS causes compromises. How are you finding Growly Notes?