For example any JS change may cause client issue, the point is you never know what may happen, because Moodle is designed and tested without these caching hacks. If you know what you are doing you can use these tweaks - you may get really significant performance improvements in case of 1.9.x, but you might end up reporting bogus errors that developers can not reproduce.
Current Moodle 2.0 code should work fine without any Apache caching hacks, it was not tested with these tweaks at all as far as I know.
Petr