Is there any evidence that the Litecoin network is significantly affected by botnet mining? Litecoin uses a hashing algorithm that, so far, is best run on CPUs rather than GPUs. 

Because most computers are not purchased for gaming and don't have powerful GPUs (which would have been useful for Bitcoin mining, at least until ASICs arrived on the scene), it would probably be far more profitable for a botnet to mine litecoins than bitcoins.

At the current Litecoin/Bitcoin exchange rate, the total litecoin network generates 216BTC worth of litecoins per day in block rewards (the Bitcoin network provides 3600BTC/day), which provides a substantial profit incentive to someone running a botnet.

Is there any evidence that botnets are responsible for a substantial amount of litecoin mining? Could this be detected?

Is there any known malware that mines Litecoin?
I have the privilege of answering your question a year later, where GPUs have taken over Litecoin and all of its derivatives. Currently, botnets would be better off mining a CPU coin like Primecoin.

That said, there is evidence of botnet mining for both Litecoin and Primecoin.