Waterproofing leather bike shoes
I wouldn't use silicone spray to waterproof leather, I'd use a leather boot proofer like Nikwax (the original product, not the brand). The spray is unlikely to damage the shoes but isn't very effective on smooth leather. Shoes that aren't designed to be waterproof often don't get perfectly waterproof even with treatment - stitching may leak and you'll certainly get water in around the tongue. 

Whatever you use, be sure not to get it on the soles, as it makes them slippery.

I've found waterproof shoes to be a bit of a pain on the bike - water runs down my legs and fills the shoes. Shoe covers help with this but then you don't need waterproof shoes. In hot weather free-draining shoes can also be more comfortable.