Let’s imagine I decide to go with 1 node per 1 HDD route and have a server with 4 HDDs and 4 nodes on the same IP address. If one of those HDDs suddenly fails unrecoverably, will other nodes receive penalties for their reputation or will they continue to work normally?
Nope, reputation is separate. Otherwise other nodes would be punished if an unrelated HDD fails. Luckily that’s not the case. Apart from sharing incoming traffic nodes run entirely independently from eachother.
Reputation is measured separately as @BrightSilence says, but it is correlated in the sense that if, let say, a hardware failure, power or ISP outage disables all of your nodes, all of them will get a hit to their reputation. This sounds like a trivial thing to mention, but still should be taken into account if you don’t want to be let down by random events.