QSYS fails to generate SS_n export correctly for SPI interface?

You would have to edit the HDL and the symbol file since it is getting generated with a single bit ss_n signal. I have never modified a symbol file directly but it's probably possible with a text editor.

If you used Quartus II to generate a new symbol based on the edited HDL you'll end up with a symbol that doesn't look anything like what Qsys is generating (but that's an alternative to hacking up a symbol directly).