Hamsters seem to enjoy remodeling their habitats to their liking, especially Syrians (though not sure your species). I put all my water dishes on ceramic tiles as I keep a few in my cages just in case my hams get too hot and need to lie on a cool surface. Personally, I would put the shelf back as hamsters generally enjoy climbing about on things, plus it's good to hold the bowl so it won't soil the bedding. I wouldn't worry about the food spilling in all honesty. Many hamsters prefer eating from the bedding rather than a bowl anyways! I wouldn't really worry, many of my hamsters have been whirlwinds and will need to have items in their cage fixed in the mornings. A bit annoying for us, but as long as they're happy and healthy, there's no need to worry
Best wishes