The lack of distinction between neuter nominative and neuter accusative is not just true of nouns in old IE languages. It's true of all grammatical categories in virtually all modern IE languages too (with some very obscure exceptions). Consider German articles der/den vs. das/das. Or English pronouns she/her vs. it/it.
More info: https://latin.stackexchange.com/questions/18/accusative-equa...
https://linguistics.stackexchange.com/questions/9105/why-do-...
Apparently one of the obscure exceptions is the Russian word оно - but they are indeed quite rare.