The below picture is of a storage system that I found online. Many churches that I have worked with have developed a similar type of system for their facilities. The general idea is to have a security cage to lock up your valuable musical equipment. You can establish multiple different policies that work well for your congregation. Some suggestions are to place a pad lock on the cage and only allow one or two people to have access to it. If someone needs their equipment then they would have to work through one of the key holders. Another way would be to put a combination lock on the door and give to code to all musical related employees or staff. In this scenario it might be a good idea to change to combination on a regular rotation.
Here is a list of a few places to check out: