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I assume you have the Nook First Ed. The Nook Touch treats side-loaded content the same as B&N downloaded when it comes to search for titles or authors. To search you just touch the bottom of the screen and "find" comes up as an option and you type in what you want and a list will come up.
I don't know how fast it would still be be with 10,000 files but I have about 1500 on my Nook, on the device and card, and don't notice it being any slower than when I had just a handful.
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