If you have reason to believe they are, you explain that reasoning to a court and if the reasoning is sufficiently persuasive the company can be compelled to provide internal information that could show whatever is going on.
Hiding this information or destroying it typically carries personal penalties for the individuals involved in it's destruction, as well as itself being evidence against the organization. "If your company didn't collect this information, why are four IT administrators and their manager serving 10 years in prison for intentionally deleting relevant business records?"

The courts are allowed to go through your stuff.

They're making money aren't they? They have to be doing something weird.

Investigation, witnesses, gather evidence, build a case and present the evidence. Same as any other thing.

I don't get why this would be harder to prove than other things?