NTFS is more secure, and I believe but could be wrong, faster. It is also more reliable than fat.... I doubt you will see a massive decrease, but a little.
To be honest hardly worth the effort I've never had any problems with FAT32 formatted drives, yes they're not as secure but for 99.9% of people that really doesn't matter, unless its a works PC I'd generally format it for FAT32 so I can fiddle with it in DOS easier.
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