This has always been the case - even before the TPE days when the downtown airport was used. It used to be a hand search of the bags. Now it is more automated.

I think the Taiwanese attitude is that they do not want their bags opened when they are not around. So, this is the way it is - you can be there if they have to open your bag - and that rarely happens. Maybe they were going after something that day?

It is a lot better than the TSA way in the US where in many airports you don't see them opening your bag and they just put a piece of paper if they open it. I am sure the Taiwanese would be very angry if this was done to them.

All that said, I am not sure what they are trying to catch and if they ever catch anything.