Be careful, synchronization on app closing (eg. Windows shutdown) can lead to data loss.

Would like to have a native API (not web) for working with doogiepim, for example, through a plugins.

This will make doogiePIM a much more powerful tool.

As an example, important features that are already available in individual completed products.

You can try to solve all the desires of the user in one product, but since each direction requires continually developed and it can lose in quality and possibilities.

but I don't like the idea of having open text, unencrypted files hanging around a disk structure

If the user needs it, probably he can already solve it himself, for example, with a mounted cryptocontainer (disk), which is compatible with iOS and Android. I do not suggest cutting out database support.

I admit, studying elisp in order to properly configure emacs is not one of the most pleasant and it becomes a problem in itself... Moreover, the org mode does not imply WYSIWYG editing.

@BiteSpire Consider ideas from this: zim-desktop-wiki
They use a simple text format (Markdown) that allows search the contents of any program, even windows + backup is implemented through git (may seem controversial, but it doesn’t bother the user).

I hope you prefer a simple, open formats for yourself and users.

Will have to use emacs, with its org-mode, browsers and other...

One file is convenient to transfer, but this does not cover the risks of possible loss of information or bugs with your software or format.
Regular files in a reliable file system are much safer.

As a database option, can be consider mounting an image with a file system, which is also convenient to transfer.
Additional data and indexes can be stored in an auxiliary file.

But, of course, your own database format is a good way to retain customers.