My current setup:
- I use an Onyx Boox Note 2 to take handwritten / drawn notes when I feel a strong need to do it digitally. It has an ePaper screen that's super smooth. The notes stay on device and are backed up (but not synced to my Tiddlywiki)
- I keep a tiny paper notebook with me at all times for jotting down ideas and thoughts that appear in my head during the day
- I copy abridged versions of my paper notes into Tiddlywiki at the end of the day or the week to reflect on them and to have them be indexed and searchable.
This solves the awkward problem of handwriting recognition being utterly unserviceable for my handwritten notes, ensuring everything that matters is searchable since I copied it manually. It isn't too much work.
During export Trilium fixes the internal references to standard HTML links so they reference pages in the structure like "./sub-folder/my-topic.html" (but yeah, it was not always like that).