None of the bears suffered serious injuries beyond broken bones and whiplash, but they were killed and autopsied afterwards. The paper doesn't explicitly state how many bears were used, and I think hundreds might be an exaggeration, but at least a couple of dozen bears were used based on the number of tests run.
There were only 7 tests done using bears, and one using a chimp.
It seems like it would be prohibitively difficult to source several hundred bears when you only plan on doing a few tests. You have to buy them and then you need to find somewhere to put them. Even if money wasn't an issue (and likely wouldn't be on those Cold War budgets), just the logistics of the problem would make it unlikely they'd source more bears than they needed.