What should I do about Deprecated Functions?
All you can really do is log an issue or PR. You're right they don't hurt anything but yes they'll need to be fixed by the extension/core eventually.
If you want to turn them off temporarily you can hack CRM/Core/Error/Log.php to just return instead of logging them, but of course they'll come back when you upgrade if they aren't fixed yet.
I'll note though that the logging is also there in the situation where it was marked deprecated but it's not known fully if anyone has a configuration where it's used, and so the hope is they'll report it.