The downside to microchipping an animal, is the number of brands that make the microchips. Each one has there own scanner and not every vet will have every brand.
Something I have seen done is having a pet tag (like what you would put on a dog or cat collar) attached to the horse's mane near their bridle path. The tag is tied into a braid near the top of the mane. It could identify the horse's name, their owner and a phone number or something.
Every solution has pros and cons, microchips could work, depending on the brand of microchip and the scanner needed to detect it. A halter could work well for catching, but can also get snagged or possibly lost (same with an ID tag in the mane). Spray painting the side of your horse could work, if you had the time, your horse catches easily at all hours of the day/night and all weathers, but would it wash off?
Whatever works best for you and your horse is the best solution. Good luck. I have lived in tornado areas and understand your concerns. I also lost my childhood horse to a bolt of lightning in one of those areas, found her laying with her head downhill in the pasture right after the storm passed :( Posted via Mobile Device