You make a (several) good points. I primarily work in Ruby and it's true that comparing a potentially complex object like a hash based on whether it serializes identically essentially means that you're comparing by value instead of reference. Depending on what you're doing, that's either really convenient or a nightmare. Ruby seems well adjusted to tasks where accessing a hash as a value is a feature and not a bug.

And for those times where you're interested in comparing instances of a hash, every instance of an object has an object_id getter:

a = {k: 1}

b = {k: 1}

a == b # true

a.object_id == b.object_id # false

Of course, this is a lot of typing, so Matz also gave us:

a.equal? b # false

Ultimately, this is what I love about the diversity of a pluralist language ecosystem. The polyglots will always win.