Hi Andy,
I haven't run across this problem in context of a bike shop, but we had a similar issue when my friends and I were running an infoshop. Even having keys for our core voulenteers became too much of an issue. We were all trust worthy and worked well together, but at one point we had 15 keys floating around with no accountability. No one knew who had one, who had been copying them, or what was expected of the people who held them.
A few things I've realized from revisiting that experience:
Limit the number of keys. A policy that grants a key to anyone who puts in enough time will eventually create so many keys that it will become pointless to have a lock at all. If a person is trustworthy enough to access the shop in the off hours then they ought to be connected enough to get in touch with someone who can open the shop for them or loan them a key for the day.
Find some way to disconnect key holding from status in the organization. This essentialy has to do with the culture of your shop and how being a keyholder is perceived. Sounds like right now having a key equates to a privelaged status and you're looking for ways to open that up. If you can find a way to make key holding more of a responsibility than a privelage, less people will want to do it. The most obvious thing I can think of is a requirement that key holders must staff a set number of shifts every week or month, and a minimum of organizational meetings. Maybe yall can think of others. A requirement that key holders clean the bathrooms comes to mind. This also creates a situation where key holders, regardless of background, become more trustworthy due to their time and energy investment in the shop.
Finally I would add that if enough people are needing to access the shop during off hours then perhaps it's time to consider expanding your open hours to reflect this rather than expanding the elite circle who are allowed to use the shop at any time. The best models I've seen so far have included a distinction between open shops where anyone can work on anything and voulenteer shops where people only work on shop projects. This frees up time for personal projects for the people who would otherwise spend all of their shop time voulenteering, and makes it a little more clear who's putting time and energy back into the shop.
I hope that all came across all right. Obviously it's not all the solutions to your specific situation, but maybe it can be some useful things to consider.
Best wishes for yall trying to work this out, it can be a thorny one.
-UGG
Spokes N Folks, Springfield, MO