Exposing the sand to trimethylsilanol would be even better. Why is it not a commonly available paint-store-type chemical?
Edit: The hydrophobic sand has numerous beyond-just-a-toy uses. Including never-freezing foundations for arctic areas and not-getting-wet fillers for buried stuff (e.g. junction boxes, could it be used for a weapons cache too?).
How do you clean the glass without tossing out your hand-crafted sand?
Perhaps pouring out the water-sand mixture through a strainer (and recovering the sand), then sacrificing the minute remains of the sand in the glass by conventional washing? Kind of similar to recovery of a solid-state catalyst from a process?
Sounds like work. I just went through the process to make it waterproof, now I have to dry it again?
The waterproofing will do the job for you, all you have to do is holding the strainer. 
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