They are not removed by removing buff effects because they have no time limit.

The correct explanation of what mysteries like skewering/sand dust do would be: 'it decreases by 10 rounds the duration of any buff applied to the target ninja'.

That's why those buffs are not removed, because their duration is unlimited as long as the ninja is alive.

The reason why barrier buffs are not removed by them is because their effect could be actually explained this way: 'as long as the barrier is up, before each action the buff granted by the barrier itself gets casted on the ninjas that benefit from it'.

This way you can actually consider that their buff is actually removed by skewering or similar effects, but before the following action gets applied again on the ninja.