I have noticed that ants can loot through the floor from three floors down.   I built my base three story base on top of scaffolding that is tall enough to walk under.   I placed my food chest on the top floor of my base.  The ants were still able to loot the chest  while being on the ground under my base.  This should not be possible.  I think this needs to be addressed.

This is a known issue and there is no word when they'll fix this. 

What I did was create barriers between the ground level and the boxes containing the valuables. I made a "safe room." 

Placed scaffolding or a wall under the container and this seemed to have worked for me. I have multiple bases and I did it a bit differently in each so I would try this. 

Just experienced this tonight... Had my food crate on the 2nd floor of the inside of my base. Ants got in to a fort then at the 1st floor was looting my food... Hopefully they fix this soon

 

I don't put food in storage containers and never have problems with ants over running my base. Just something to think about since they seem to only target food.