I agree no system is perfect, but to some extent that's the job of enterprise risk departments in auditing firms: They look to determine who has access to the accounting databases etc, whether those accesses are logged and traceable and so on. They also look for discrepancies in the way those databases are managed and if they find them are obliged to recommend a more thorough financial audit rather than relying on electronic systems. If the entire company is systematically deceiving them then there's little anyone could do (other than whistleblowing).
The biggest problem with auditing is LLPs: Once upon a time they were personally and professionally liable for their work. If they failed to audit something correctly they were liable for a huge amount of damages, and because of that had an interest in ensuring no-one deceived them. LLPs reduce if not remove that liability (the personal liability of partners in the company at least - the company as a whole may still be liable I guess) and so there is less danger if they mess up. Couple that with a competitive market that means an auditor who finds too many problems will likely not be getting the contract next year in favour of a more 'flexible' competitor and you don't have an environment that encourages rigorous and cautious auditing practices.