> do you store them compressed or plain?

Can’t speak to your other issues but I would think the right file system will save you here. Hopefully someone with more insight can provide color here, but my understanding is that file systems like ZFS were specifically built for use cases like this where you have a large set of data you want to store in a space efficient manner. Rather than a compression dictionary, I believe tech like ZFS simply looks at bytes on disk and compresses those.

By default, singlefile only saves when you tell it to, so there's no worry about leaking personal information.

I haven't put the effort in to make a "bookmark server" that will accomplish what singlefile does but on the internet because of how well singlefile works.