That's really the purpose of how DMCA is set up. It gives websites that host files uploaded by third parties a way to respond to copyright violation claims that removes their liability. They don't have to act as an arbiter, they can simply act on the claim and then act on a counter-claim if the claim is disputed. YouTube is a little different, because they take it on themselves to look for potential violations ahead of time, but the benefit of being able to host unknown content without liability is still there.

Whether a company follows through with a lawsuit once they get a counter-claim is ultimately up to their priorities. Though I imagine the number of people who ever bother to file a counter-claim is probably vanishingly small. But if a company the size of Sega is bothering to send DMCA notices in the first place, I don't think I'd bet on them ignoring the counter-claim, personally. Any counter-claim they ignore is an argument for public availability and thus fair use.