With most horses the clicker is going to work for a brief period and then the horse will completely ignore it.
I always take a trash sack with a bunch of Pepsi cans in it. I will tell my assistant (wife) when I'm ready to shoot and then she will shake it. Usually works.
Make certain that you try and have the horse's ears up in all the portraits. You won't catch them all that way - the horse is just too fast at putting them back - but your client will like the ones with the ears forward a lot more.
Try and get an idea how the horse is going to react to your fill flash ahead of time. If I am working with quarter horses or other "cold bloods", mostly western type riders, I will just start firing away with flash after we pose. With thoroughbreds or other "hot bloods", mostly english type riders and hunter/jumpers, will often fire a flash from a distance and then gradually move it closer and closer firing it until I get the final distance.
I will always tell the client I am going to use flash or more often I will ask, "How do you think your horse is going to react to flash?" This is strictly for liability. I have put the onus on him/her. I have never had a problem with flash and horses yet.
And, yes, as Gonzo mentioned it is good if the client gets the edge off the horse before the shoot. The problem then is that the horse may be sweaty. Generally walking isn't going to do much. I usually ask that the client longe or lope (your client will know what these terms mean) the horse to get the edge off before I get there. And early enough that your client can clean up the horse for the shoot.
When shooting a horse use the same logic on focal length as you would with a human. If you use a wide angle it is going to elongate the horse and this is just as offensive as it is in a human portrait. An elongated body is a conformational defect to horse people, especially western type horses/riders, and should be avoided.
Have fun at your shoot and sorry about the late response. Just saw this.