@tigran:
Yep, you can safely delete the linkss folder once it's uninstalled
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On the other hand, that *really* shouldn't happen, because, as you guessed, at the core, it's only a simple bind mount, and nothing else.
The only thing that runs in the background is the USB watchdog, and it might very well be going wonky on some (broken?) setups, and end up in an infinite loop churning the CPU; I've tried to avoid/workaround it, but it's still quite possible. I'd need a bunch of logs, and even better, a top/ps output while experiencing the slowdowns, to investigate this further, though
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One 'quick' way to check if it's indeed the source of the issue would be to disable the 'autoreboot' feature, and restart you Kindle.