No, you will not be able to use FTP if your card reader fails, both (WiiuFTPServer, as well as FTPiiU) requires that their respective files be on your SD card to be launched.
Even with Autoboot enabled, your SD card reader is still required. When you enable autoboot with Tiramisu, a file gets created "wiiu\environments\tiramisu\autoboot.cfg" , and within it it stores which option you selected to autoboot. This file is accessed everytime you boot your WiiU.
I'm with you man.. I too think this would be a very rare situation...(
link1 ,
link2,
link3,
link4,
link5 ) . For me personally, I picture things like SD cards mistakenly being inserted upside down by your friend and bending the internal Wiiu pins... Or if any of you have kids, you'll know that there's no place in your house that doesn't have a cheerio shoved into it. ...
Anyways, I'm not trying to derail any of the awesome work that is being done here. I just think that if you already took the time to get your DS game , there's no reason why you can't leave just Haxchi behind as a backup in the unlikely event that something should happen to your WiiU card reader
To each their own! Cheers!