Proofs of reserves & unexplained strange movements of funds will get published if they're audited.
And how do you know the proof of reserves is accurate? What's stopping an exchange taking out a loan the day before an audit and paying it back the day after? Or borrowing funds from one of their affiliated companies or entities? Or even just the CEO topping up the exchange wallets with their own funds prior to the audit. This exact thing has happened before with Bitfinex handing hundreds of millions of dollars of crypto to Tether on the very morning of their independent audits. And yet USDT continues to have a market cap of $65 billion, despite being a fractional reserve scam. Proof of reserves proves nothing.
Also one of the main risks is anyway that the money is stolen by somebody that works at or owns the exchange. It is more simple than you would think because they own the keys, and coins can be mixed and sold worldwide. It is basically the perfect crime to disappear with stolen bitcoins.