We do. We have a daily process which crosses information between our inventory, CMDB, Antivirus console and AD. This is quite tricky if you have a huge number of devices, but it's key to have an idea of you overall systems status, and also, to keep tracked those devices which can be out of control.
Cross checking your inventory tool with AD is a necessity as it's the baseline (starting point) for a Microsoft true-up or audit.
That said AD is only a subset of the data and will not always contain UNIX, Linux, Mainframe or MAC devices. Servers can also be mising as can virtual hosts (VMware), public facing networks and workgroup machines.
At a minimum you should be able to reconcile all AD entries for the last 30 days with your inventroy tool. Comparing your inventory tool with what Microsoft MAP (free tool) is the easiest way to do this as all licensing tools support MAP data.