If linking between ideas and including images / screen captures are important, Ulysses is going to be frustrating for you to use. The real question is if that is something you think is cool or is something you use in your daily activity. Tagging, filters, and sheet / group organization will drive how you manage it.
It is worth the effort to glance through their tips and tricks section for tidbits. I’ve purchased but not watched Shawn’s course, so not sure how much is covered there.
The collapse group feature solved my major issue with the app, archive vs. active content.
Move old notes into an “Archive” group and have all the live ones in another. Collapse to just live and search is restricted there. This also allows you to mass filter out work or personal items from each other when searching / applying filters.
Ulysses is where I do all of my writing, journaling, where notes end up, someday / maybe lists, commonplace book, etc. I was even using it for project / task management before switching to paper.
If you use an iPad with external keyboard - nearly all of the desktop app functionality is present with keyboard shortcuts. You can drive 95% of the interaction from the keyboard. Command + O all day.
Nothing wrong with having a writing app and a notes app, especially if you create any resistance to writing because of random notes also being in the same tool.