Folding@Home ONLY uses idle time. If the server is actively doing something,
anything, it's using a higher priority than F@H is, and will not lag. I run F@H on my PC's and it doesn't lag them down.
The HDD's are limited by power, SATA/IDE connectors, and heat. You could add as many as you want, provided you add additional SATA/IDE cards and keep the case cool and have plenty of power.