Question: Is there a max limit on JKDefrag as there is on MS Windows?
No, there are no limits. If you have a huge number of files on your disk then your computer may run out of memory, though. JkDefrag needs about 600 bytes of memory per file.
Will JKDefrag do anything to mess with the HDDs if I run it on that configuration?
From the frequently asked questions: "JkDefrag is based on the standard defragmentation API by Microsoft, a system library that is included in Windows 2000, 2003, XP, Vista, and 2008. Most defragmenters are based on this API, including commercial defragmenters. Basically all JkDefrag does is send "move this file to that location" commands to the API. It does not touch the disk by itself, and is therefore extremely solid. If your disks use NTFS then you're even safe when the computer crashes in the middle of defragmenting. Nevertheless, it's still a good idea to backup before defragmenting, just like with other defragmenters, because the heavy use of the harddisk may trigger a hardware fault (disk crash), and/or overheating (disk, power supply, controller chipset, etc.)."