Private companies don’t have to follow the government announcements. The company is open, if employees choose not to turn up then they either use their personal leave or dock pay.
Drag up an old thread, Salary deduction due to the typhoon holiday?
Old news, don’t know what the result wa, https://taiwantoday.tw/news.php?unit=10,23,45,10&post=15372
More up to date news, http://www.taipeitimes.com/News/taiwan/archives/2018/07/11/2003696482