Whether it’s correct or not, it’s not a great sentence, and would benefit from a rewrite.
Language is weird sometimes, so I’m not certain, but your argument seems circular and incorrect. Use of ‘is’ doesn’t cause ‘data structures’ to be singular a collective noun. The noun is plural, so the correct verb is ‘are’. The sentence would need to name the singular collective in order to use ‘is’. For example: “A set of data structures is how we store and access data.” That would be correct. Arguing that “Hard disks is how we store and access data” is correct and that “hard disks” is a singular collective noun, because the sentence used ‘is’, is not normally accepted grammar.
Normally I try to get past grammatical errors in scientific literature if they do not affect the meaning of the content. Authors may not be writing in their native language, and the literary aspects of the piece aren't its purpose. When it's the third sentence in the abstract and the first of two questions that the paper is fundamentally seeking to answer, it does make me twitch a little.
Yes, absolutely. Why do you have to ask? Unless '-s' is its genetive inflection, something German for example has preserved, or something weirder, it is a crystal clear mistake