"For the places that have tools, how are they presented / made available to the hourly renters? How does the shop keep tools from being stolen?"
They have bays, and small drywalled 'rooms' directly off the bays with a seat, a table, a rolling cart, a tv, vehicle fluid containers, and a big tool chest. The tools are separated into draws by what they do: screwdrivers in one, pliers/channel locks/etc in another, sockets in yet another, and so on. Within each draw, things are also separated into standard and metric.
There's usually a front desk person working, as well as one or more mechanic on duty, so there's a tad bit of oversight. To be honest, I've pretty much been the only person there every time I've went (I try to go as early as possible, though), and the mechanics haven't really paid attention to me too much. They definitely don't do inventory or look through the vehicle after you're done. My assumption then is that they just trust that no one's stealing anything.
I will also say that there are 3 ways of working on your vehicle. The first is by yourself, but the second one is working alongside a mechanic, so they have the ability to keep an eye out for stealing. The third is just to have the shop do it by themselves, of course.