Here's the thing though, doctors have a long storied background of not knowing what the hell they're doing. History is filled with stories of hilarious medical ineptitude, and in all likeliness, today's medical practices will be similarly snorted at 100 years down the road.
Empty definition, containing nothing; having none of the usual or appropriate contents: an empty bottle. See more.
On an empty stomach usually means when you are sure that you haven't eaten anything for a time long enough to empty your stomach. When everything you ate you are sure is already digested and excreted. The best time to take such medicines is when you get up in the morning before the breakfast.