Waterproof shoes can really come in handy if you live in an area that gets a lot of rain, is extremely humid, or if you plan to do some running along a beach, lake, or beside a body of water. They would be a good investment if you refuse to run indoors on a treadmill in the chance of inclement weather. But as you have noticed, they can be an expensive purchase. And running, even though it can be a very cheap hobby to have, can also be very expensive when you start investing in different clothes for different seasons and purposes, gadgets and technology, and more than one pair of shoes for your training. Unfortunately though, aside from just flat out buying waterproof running shoes, there really is no good way to waterproof your existing shoes. There ARE a few tips and tricks to help out, but you likely will not get them one hundre percent waterproof without sacrificing some of the integrity of the shoe.
If you are currently running in lighter or more minimalist shoes, then you are already ahead of the game. Less surface area means less opportunity for your shoes to get soaked. And the more rubber, the better (although you would then sacrifice some comfort, and your shoes would definitely be heavier and more difficult to run distances in). You can also choose to duct tape the mesh and fabric part of our shoes. Duct tape is water resistant, and can help keep moisture out. But doing this will (again) add unwanted weigh to your shoes, and might not be as comfortable and cause the shoe not to fit your foot as well. (Plus, you might get some strange looks...)
For the most part, a decent pair of running shoes, even if they are not specifically waterproof running shoes, are designed to be able to withstand the occasional drenching. Running shoe manufacturers know that runners are hard core, and typically do not let a little rain and a few puddles stand in the way of their daily runs. So they make sure that, even if they are using fabric, that the shoe can maintain its integrity when wet, and that they dry out quickly and with minimal smell or stench left behind. After all, our feet are producing water through sweat every single time we run! Companies know there has to be at least some level of waterproof-ness when it comes to high quality running shoes.