Update: a cop came yesterday and talked to my boss. From what I've heard from other employees, they're not interested in asking us any questions, the cop basically said he thought it was an inside job and told our boss to keep an eye on us employees.
She changed the locks, took all of our keys, and is not giving any of us keys.
This sucks because she keeps fairly irregular hours and is not always here to unlock in the morning (so we'll have to sit and wait for her), and I work an odd schedule too (including weekends sometimes) because I also go to school full time. Working 40 hours just became way more inconvenient.
She also said that this means there will be no christmas bonuses next year. Doesn't bother me, I'm going back to school before then, but it sucks for those who are staying.