The place to stop the water is before it reaches the plywood, not after. If the plywood gets wet it will not dry out, it will rot. Seal the grout. However, to answer your question, the silicone will not cause buckling of the floor.
Sounds like you might be a little light on the substrate for tile, you've got 5/8" or 3/4" plywood sub and then 1/4" plywood? You should really have a minimum of 1-1/4" of plywood in most applications. (Standard 16" o/c joist spacings). Did you already or are you going to thinset under the cement board?