Hi @F-EverNt, welcome to the forum.
1.) Is software such as Joplin ever done? Joplin on Android is usable enough for my needs. Try searching online and through the forum to see if your specific needs are met on Android. Explaining your needs here or trying Joplin on Android yourself are also options.
2.) Markdown takes 10 minutes to learn, if that. Check out the Markdown Guide, the Markdown Tutorial, and/or the creator's original guide to learn it. You can take what you learned and use it not only in Joplin, but in this forum, and elsewhere too.
3.) Forum threads like Requesting encryption of local Joplin data (at rest encryption) and VeraCrypt encryption of Joplin profile explain why Joplin doesn't come with encryption at rest and how to pair it with other tools to achieve encryption. If they don't answer your question, feel free to explain how and/or search for better answers.
4.) Check if File > Export all > HTML - HTML Directory exports the structure you want. Otherwise, these resources may help (if they aren't outdated): Export Directory Structure - #3 by dpoulton and Export all with index in HTML
Someone please correct me if I'm wrong on any of the above.