5000 Chinese spies in Taiwan

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.”