I think that's fine if there's a legitimate security concern and that's what the information is used for. However, if the information regarding when employees are in or out is given to managers so they can keep tabs on them, I feel it still shows a profound lack of trust.
If one's employees are really that bad, then maybe their managers should check up on them (via phone calls, stopping by, or asking others to stop by their desk, etc.) on a case-by-case basis if they suspect a problem. If there really is a problem, then they should be dealt with.
I see no value, however, in the routine tracking of exempt employees. In this day and age, more and more work teams are spread out across the country. I've often had staff working in different locations from me, at one time my entire staff was 1800 miles away. I believe you judge exempt staff by their work product, not by the hours they put in. How many of us, for instance, may spend an hour over the course of the day making silly posts in the Cooler, yet spend much of our commute on our Blackberry and work on work projects on home over the weekend.
A good manager will know who the good and bad performers are on his or her staff.