Hmm I’m not really sure what caused these cracks in the first place? Looks to me that you have a problem with overall poor craftsmanship, because even if stone on the floor has cracks under your drain there should be something called "cuff" or a "sleeve”. It is made out of plastic or some similar material, circle like shape with diameter bigger than drain, whose inner side goes inside the drain, and outer is connected with hydro insulation. Purpose of this element is to prevent situations like this. Long term solution is to change, at least partially stones on the floor, and this time with a sleeve. When it comes to short term solution and your plumber advice he is partially right: Silicon is a perfect surface for mold, especially in a rooms with high humidity level, like this one is, plus it is organic so it disintegrates. You can fix the leak with silicone, but you must change it from time to time (let’s say once in a six months, or when it turns black)