My first thought was predators. There are many animals that feed on fish: raccoons, skunks, otters, snakes, turtles, and water birds. A 3' deep pond helps, but providing koi with underwater tunnels to hide in is also helpful. Some people lay welded wire fencing over their pond to keep larger predators out.

Is your pond new? During the first year a number of environmental issues can cause koi to die. Water quality, parasites, etc. can all cause more damage in a new pond no matter how well the pond and its systems are constructed. No one is able to diagnose a cause, but every expert agrees that New Pond Syndrome is real. Could your missing fish be rotting on the bottom?

Koi are much more common now, but some fish colorations are considered more valuable. If the missing koi were rare types they might have been stolen.

Fully agree with everything mindshift said. Look for dead rotting fish and if you find none, I'd assume predators or theft.

Stolen unless your pond over flowed and they some how jumped out ..My brother had his stolen and eaten by his neighbors.

I'd invest in a mini camera remote that you can see from your phone or in some kind of scare tactic.

"and eaten by his neighbors." Oh. My. Gosh. That's shocking. And disgusting.

Knowing what part of the world you are in will help.... But if you aren't seeing any scales or fish pieces near the pond (Which raccoons or other land varnmits would leave around).... Then it would be a heron ... Who just eat the fish whole and leave nothing behind.

I will ill say though... In years past when a herons has struck my ponds... The remaining fish are beyond skittish and hide ... Barely coming up for food even. What are yours doing?