For my rig I am going to be building this summer, I am going to initially go with the Kingston HyperX 3K because it is a really solid SSD and will be much faster than a standard HDD. However, I will only be getting the 120GB model, and I will probably want to install a secondary hard drive at some point. My question is, will installing that secondary hard drive slow things since it wouldn't be an SSD?
No it will not slow things down.
I have that same SSD. Boot and main applications on it. another SSD for other apps, and a couple of HDD's for mass storage.
But a 128GB + whatever HDD will work just fine.