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IIRC one of Monero's design goals is that it isn't easily GPU/ASIC-mineable, so CPU mining is competitive. It's also designed to be difficult to trace.

Both of these properties make it a relatively safe and profitable avenue for malware authors.

Mining with JavaScript or WebAssembly is no longer viable as being competitive now requires using a JIT compiler.

Nothing can really be done about it. Pool operators can ban the wallet addresses of known bot masters from connecting to their pool, but you can't really ban someone from participating in an anonymous decentralised network.

Maybe it's to do with the fact that monero tokens are non-fungible, unlike some other crypto-currencies.

I think you mean 'fungible'. Non-fungible means 1 XMR is not equivalent to another 1 XMR. The use of ring signatures, key images and transaction amount hiding gives Monero its fungible properties. This makes it computationally difficult to trace a particular transaction graph. This provides fungibility beyond that of Nakamoto style coins, in that you cannot easily block/identify addresses or transactions.

Monero is likely the absolute most fungible cryptocurrency.