I would ignore such warning message if Electrum can run normally. In fact, many application (and even your OS) will show few warnings, but usually you can run it without facing any problem.
If just now you had installed the urllib3 and chardet (and any other dependencies) packages from APT, and you're sure no other program/library is using it, then uninstall them and use pip to install these dependencies, which should be the latest versions since Python 3.7 is still supported.
urllib3 is
most popular package (see
https://hugovk.github.io/top-pypi-packages/). If you uninstall urllib3, many application/library will be removed as well and could break the OS.