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This is solvable by adding big huge warning that ADB is running. Not by removing feature.

That huge warning would also be permanently shown for everyone using Shinzuku apps. I think that UX would neither be desirable nor increase security.

..for the very little number of people who use them?

Arguably it would be highly preferable compared to the option of not being able to use them at all.

Just use opensource phone os!

android is open source