That'd ruin one of the greatest benefits of malware targeting GPUs: in almost every OS's default task manager, it does not display GPU activity. With reasonable intensity settings (which Scrypt mining requires on most cards to prevent HW errors, anyway), it would be almost impossible to detect, especially considering how many people stuff desktop PCs into little desk compartments (minimizes noise, but would help prevent them noticing the high heat and noise from GPU fan going @ 100%).

What'd indicate a botnet is a steady hashrate cycle, where at some times, very regularly, hashrate dips and peaks, which is the expression of people turning their PCs off when they're at work or sleeping.