Man-In-The middle attacks can be avoided by verifying your connections RSA Key Fingerprint. I keep that posted on the website. Could this be forged...I suppose anything is possible. Those that are paranoid enough to not trust SSH alone should sleep better knowing they have the option of adding a second layer of defense...EncFS or TrueCrypt...or anything else they want to incorporate.
A good practice would be to use a different password for accessing your SSH account than that of your Pass phrase for your encrypted Data. Personally I feel those two methods combined provide Excellent security for your Data.
Loss of performance with Encryption... I don't see this being a noticeable difference. The only downside I see is maybe a little extra leg-work because there is an added level of complexity. Some folks for example that are only storing their music collection may not worry so much and just prefer to keep their storage solution as simple as possible.
You can back up your whole computer. However, if you want to copy every single file...you can run into issues with locked system files and such...(Particularly on Windows Clients). If you are referring to backing up your computer as a "cloned image" for instance....I wouldn't be able to help you there. That's probably possible, but also probably fairly difficult to get going without some paid software...or a lot more legwork. Personally, I think a more ideal solution is to arrange all your important/critical data into a folder, and then duplicate that locally if possible. Then the last leg of the backup would be offsite storage. That way local restores are quick and easy...then offsite data is there in the event you lose both...or there's some sort of disaster/theft/etc... at home.
I hope I've answered your questions...if you ever want me to help you with anything specific just let me know. Sometimes I'm quick to respond and sometimes I take a little longer. I'm going to be traveling away from home in the not so distant future so during that time I may be a little more slow.