Most users should never use the SS symbol in their code. There is no need to set SS as an output. Libraries that use the SPI bus configure SS correctly unless the library has a bug.
You must not use SS as an input in your code.
In master mode, the SS pin must be held high to ensure master SPI operation if this pin is configured as an input pin. A low level will switch the SPI into slave mode and the hardware of the SPI will perform the following actions:
The master bit (MSTR) in the SPI Control Register (SPCR) is cleared and the SPI system becomes a slave. The direction of the pins will be switched according to Table 2-1.
The SPI Interrupt Flag (SPIF) in the SPI Status Register (SPSR) will be set. If the SPI interrupt and the global interrupts are enabled the interrupt routine will be executed.
I had in mind that setting the SS pin to OUTPUT was meant to indicate to the card that there were some devices that were using SPI, does it still work when you set it up to HIGH?
The SD card is a slave and doesn't care or do anything with other devices. SD libraries don't look at the previous state of SS. The libraries just configure SS as an output and sets it high.
The key thing is to set chip select for all SPI devices to output mode and high before calling any library that uses the SPI bus. Chip select for a device may be the SS pin but that is irrelevant.