Files on disk, no matter what the size, aren't going to have an effect on how fast or smoothly programs run. For the most part, just store things wherever you want. However, files on an external hard disk are somewhat slower to read and access than files on a local hard disk, so storing infrequently used loops on an external disk frees up space on your faster, internal ones. Don't do that for small one-shot samples however, because many samplers will stream them off disk during playback - and if your disk is a slow external one, you may encounter glitches. (Also, accessing USB devices - including hard disks - is quite CPU intensive, so you don't want to be doing that during playback if it's practical to avoid it.)