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Yes, but devil’s advocate: you also need a program to text files, needing a program to read sqlite files is not worse.
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I am confused by your requirements. Why do you need to store your data as json or XML? Would it suit your requirements to read in text files, convert to sqlite for processing and then save as a text file? What do you gain by being able to edit the files in a text editor, as opposed to a table editor? Do you maybe just need a config file (e.g. in toml format) and don’t actually do much data processing?
Definitely JS if you want to also have a website. Use electron to turn your website into an executable for the desktop. Python+qt is ok for Desktop apps, but does not work for a website.
Languages that compile to wasm would also be an option, (e.g. https://egui.rs with rust), but as far as i am aware none of the languages you’ve listed are in that set. (Only go would even be a contender between python, ruby, js and go)