This issue is the collision between T167653: Consider ranks in constraint checks (constraint checks look at statement ranks) and T168532: Check constraints on qualifiers and references (constraint checks no longer happen on statements, but on snaks).
Qualifiers and references don’t have ranks. Do we care about the rank of their main statement when checking them? Should we skip most constraint checks on qualifiers of deprecated statements, just as we skip them on the main snak of the deprecated statement? Or should the qualifiers still be checked?
If I recall correctly, the rank semantically applies to the claim, that is, the main snak and the qualifiers, but not the references. Do we follow that, and skip constraint checks on qualifiers but not on references?