Makes sense to me, but it's worth noting that (like any removal of APIs from headers) this breaks compatibility for thirdparty modules or platforms and user forks who may make use of it.

I'm starting to think that we may need to collect information on all those changes to core headers done recently to add to a subpage of the 4.6 migration guide for C++ engine modifications.

It would be possible to add a [[deprecated]] version of the removed structures, which would save modules from compile issues. Should I add it?

Ehh, I don't think that's necessary. Though if you really want to have some contingency, appending this to the end of variant.h would suffice:

#ifndef DISABLE_DEPRECATED
// Compatibility with pre-4.6 modules.
using VariantHasher = HashMapHasherDefault<Variant>;
using VariantComparator = HashMapComparatorDefault<Variant>;
#endif // DISABLE_DEPRECATED

See also: an equivalent implementation in version.h for GODOT_ defines.

Thanks!