Yes, poor blood flow through the LAA is a cause of thrombosis. That's why you're on Eliquis and why a Watchman would be beneficial for you.
You LAA is silent because it was isolated during your ablation. It wasn't something that happened afterwards. Mine isn't silent but it's dysfunctional, and that's true of most of the people I know who've had their LAA isolated. So it may not be common, but that doesn't mean much.