CPU mined coins are subject to botnets by definition. However, this is not what you want for the coin you're mining or investing in. Large botnet share means that the majority of the coins is obtained by the scammers and is likely to be dumped. This can't be good for the long term development because the coins are spread not among the devs or users, but are obtained by botnet holders.
How much is the case for Monero? I really believe that not all of the spikes are due to botnets, but at least some of them could be.
As far as I know this is not a first botnet in Monero history. Heard something about it not so long before june. Well, certainly it’s not a Monero developers fault - they are doing the best they can.