The last time anyone looked at the gold was 50 years ago. The gold hasn't been fully audited since it was brought in to Fort Knox. That was about 90 years ago. "Audits" of the paperwork are preformed regularly, but no one has physically counted the bars since they were brought to the vault.

Are they still there? Let me tell you the story of the Canadian Strategic Maple Syrup Reserve. The reserve was set up to store maple syrup to manage (i.e. fix) prices. It works somewhat like a grain silo, only much stickier. The syrup is stored in 50 gallon barrels. Sometime during 2011 and 2012 thieves siphoned off over 9,000 barrels of syrup, valued at nearly $20 million. The only reason this theft was discovered is because the stockpile is audited annually. Even then, the theft would have gone unnoticed had the thieves not gotten lazy and complacent. When they started, they replaced the syrup with water, so that the barrels would still be heavy. After a while, they stopped bothering with the water. The weight difference is what tipped off the auditors.

Now, maple syrup is generally not as well guarded as gold, and the thieves took advantage of a lapse in security. It could be argued that security at Fort Knox is far superior, and therefore a theft is less likely. However, gold is also far more valuable. The motivation to steal it and the amount of resources that can be invested in the theft are both much higher. Additionally, it is well know that no one ever checks that the gold is there. This makes the risk of discovery much smaller. It seems highly likely that someone would at least try it. There is also the possibility of the government purposefully selling or leasing the gold in secret to keep the gold price from rising. Has security at Fort Knox been air-tight for 90 years straight? Has every employee ever to guard Fort Knox been 100% trustworthy? Have the administrators in charge (the treasury department and the mint) ever been involved in in any illicit activity? Probably not.

Give all that, it seems highly unlikely that all the gold is still there after 90 years. It also seems likely that if some of the gold is missing, then a large portion of it is missing. If you get away with stealing a little, why not steal a little more? There is very little chance that all of the gold is still there.