If they know the number of spies (and presumably the spies themselves), then why don’t they just kick them out or arrest them and charge them with spying?
They do - kick ‘em out - when they find 'em. My reading of the article suggests they’re simply - as @Rocket would say - spit-ballin’ here. It’s an estimate based on the number of cats they’ve caught, plus additional inconclusive math. To start kicking people out wholesale would be a fuckin’ catastrophic diplomatic mistake - perhaps even fatal - for Taiwan. Look at what the Chinese are trying to do to the South Koreans right now. Imagine the fury - imagined and/or otherwise - that would rain down on this godforsaken country. And as the old adage says, “Better the devil you know than the devil you don’t.”