AFAIK, 10.9.x requires a few days before it has a normal startup time....I should of timed my old start up time to compare to my new start up time but I did not. The MacOS still takes quite a while to start up compared to Windows.
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None, if you disable spotlight for those partitions, and if you have enough RAM (for the OS X file read/write caches).As I said before, I have 3 external hard drives hooked to my 2011 MBP for a total of 8 partitions. I have no idea what impact this has on the OS.