Sorry can't really help you on what or where it is, didn't the vet give you any ideas?
My mare Meg use to do the same, it never seemed to cause her discomfort, or effect her in anyway. It was just irritating. So I put her on Cortaflex, as a recommendation from my vet. And I'd say roughly within a few weeks the clicking had stopped.
It's generally an indication of arthritis or very early arthritis. A lot of time though, there won't be any present pain, but you may see joint complications in the future.
Was she worked hard previously? Such as a reiner, cow horse, barrel horse, ect?
Is there a general way that I can prevent it from getting worse? Perhaps glucosamine? I give that to one of my other horses who was a showjumper in a previous life. But my pony with the click has always been a show pony, ie: not worked very hard.
Ok have you asked your vet about it.... normally it can be on set of arthritis....or just air in the joint that needs to be releaved....we had a horse cyropactor ....never spell thing's right......at our friday night ridding class who adjusted one of the horses who was clicking in class...this man took his time to show us how every thing was done....would never do it my self.... but he went over every thing on the horses body and adjusted it...it was cool and the horse seemed a little releaved in the end...he even fell alseep at one point....your horse will be sore for a day after it's done but it will thank you in the long run....