Incidentally, English has a very similar pattern: most animate pronouns have nominative–accusative alignment, while nouns and inanimate pronoun have neutral alignment. It’s pretty common in Indo–European languages.
(Actually, come to think of it, in German only the masculine differentiates between nominative and accusative.)
That is true, but it's not really an example of Latin neuter nouns being subject to a fundamental rule specifying that the nominative case can never be distinct from the accusative case.
The rule exists, but the second declension forms are very standardized. You could equally use them to argue that Latin has a fundamental rule specifying that the ablative case and the dative case are always identical. (Though for that argument, the first declension would present a problem.)
Latin requires that neuter nominatives be identical with neuter accusatives even when the nominative form is unconstrained by its declension (only possible in the 3rd declension), and even when the nominative form is, by the standards of Latin, utterly bizarre. The neuter plural nominative of hic is haec (identical to the feminine singular, also an interesting [but not universal] pattern in Latin), and so is the neuter plural accusative. This is a word in the second declension, but it's a wildly illegal form for that declension.
And yes, as far as I'm aware, this treatment of neuters is an Indo-European universal rather than being anything specific to Latin.
This can be explained as a continuation of an old rule that said that only living beings (marked by endings such as -us, -a; -i, -ae) could be "active" subjects.
A "thing" doesn't have agency; it can't "do" anything to something or someone else – in other words, it can't be the subject of a transitive verb. It can only be either the subject of an intransitive verb, or the object of a transitive verb – and thus in Latin takes the endings -um, -a in either event.
Bonus amat bonum: The good (man) loves what is good. (Meaning 1)
Bonus amat bonum: The good (man) loves the good (man). (Meaning 2)
Bonum est bonum: What is (a) good (thing) is good.
This is exactly the same pattern as in ergative grammar: the object of a transitive verb has the same case as a thing that is the subject of an intransitive verb.