[FIX] core: improve warnings configuration

DeprecationWarning was configured as `once` which might be why I
missed some previously: `once` means the *filter* will only signal
once, meaning only one DeprecationWarning gets shown per run. Even if
there are 5 *completely different* warnings getting generated by the
codebase.

`default` should be more suitable, I think I'd originally
misunderstood it as "whatever the default is for this warning" but
what it *actually* means is "print once for each (module, lineno)".

An alternative could be `module` which would show the warning once per
module but wouldn't trigger from different warnings in the same module.

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