For that many devices on SPI, run 7 pins to an address decoder that fans out to 128. You can do this in the spare pins of an FPGA that you might have for some other purpose, and the 7 pins are cut down to one or less if you've already put much into the FPGA. For example, the FPGA provides 4096 bytes of registers (12 address bits) to the MCU but only needs 3700 registers, so use one of the spare bytes to control which SPI CS is enabled.

I've also seen JTAG as an alternative to I2C and SPI. JTAG can be part of normal operation.