Hi! I have recently bought Deepdwn and would love to switch to it for knowledge base management, but it lacks two features related to Zettelkasten methodology that are mentioned in the title.
As for good examples I will link to the other software that in my opinion is doing great in those terms (all are Markdown editors):
Zettlr
Athens (demo) / Roam Research
Logseq (demo)
Obsidian.md