the smaller tank is upside down and holds water due to the vacuum being created. the water can't leave because air can't reach there to take it's place. if there were a hole in the smaller tank, air would get in and water would leave.
my concern with the way you have it set up would be the pressure on the bottom pane of glass being localized at just those four points where the bottles are. if you could get some sort of rectagular support that spread the weight out more, i would think it would be better. i would also think that siliconing or otherwise attaching (i imagine silicone would be difficult due to the small tank being acrylic) the bottles or whatever support to the tank would be a good safetly measure. it isn't likely, but if someone leans on the upper tank, or you bump it the right way while working in the tank, or something like that, i would be very scared that it might tip over the tank and create a huge mess. be careful.