yet again i wish ppl would ACTUALLY USE FLASHFXP before making any suggestions
flashfxp had sites.dat encryption since v2.0 that's like for about 2years
if you consider your site info to be "vulnerable" then you enable password protection, or better yet don't store sensitive data.
if you don't consider it to be at risk then....it's up to user to deside if they want their sites.dat to be encrypted or not