No they're not. If you're using an array with length over a billion in Java, your code stinks already before you start using binary search.
A binary search implementation should still work, regardless of the array length, or have the limitation documented.
And of course an array "with length over a billion" can be totally valid, depending on the use case, your tradeoffs, available memory, etc. It could even be the optimal data structure for some use cases.
Also big arrays being (supposedly) a coffeee smell doesn't mean that code handling them improperly is not buggy.
Those APIs use long as their offset unlike the 32 ints used by arrays, and would avoid having to copy the data into some other object.
There has been some discussion over the years about how arrays could be changed in the JVM to support longer lengths, but doing so without breaking existing code and while providing truly useful functionality without providing obvious footguns isn’t as easy as you might think.
If your code has arrays over a billion elements, then it will fall over the moment someone inputs slightly larger data