On the HHVM blog there's a post talking about some of the updates they've made with array handling in Hackto help make it more efficient and overcoming some of the challenges in how they're being used.
Arrays are the ubiquitous data structure in PHP, used to represent everything from lists, associated lists, sets, tuples, or even a bag of data. This flexibility itself makes it challenging for Hack to understand how an array will be used. [...] If this was the only problem with PHP arrays, then the solution would be “simple”; make the type checker smarter (something we are working on). However there are a number of other semantic details around arrays that are nearly impossible to analyze statically.
They talk about some of the issues a bit more specifically including:indexing of non-existent keys key coercion arrays containing references
They also talk about some of the legitimate use cases for arrays over the collections Hack offers, mostly do to with the values they could contain. The post ends with links to some of the other future improvements to the array handling in Hack and a look further out and their vision of replacing PHP arrays with Hack arrays and moving collections to a runtime library.