AM3359 - ZCE, ZCZ differences

The packaging and pin count. See the AM335X Datasheet, Rev. F sections 2 and 7.

No, inside it's the same processor. There is a difference in the interfaces that are pinned out externally, and also the OPP combinations are limited on the ZCE package, due to VDD_CORE and VDD_MPU being merged on this package.

By the way, just noticed that you are asking specifically for AM3359. Please note that this processor is offered only in the ZCZ package. There are ZCE package options for AM3352 and AM3354 only.

How do you intend to provide the SPI_CS signals? The AM335X has only 2 CS signals per SPI. Otherwise yes, you will probably need to buffer the SCK and MOSI lines

I would suggest the SN74LVC2G07, since you only need to buffer two lines. For the chip selects I suggest you use some 3:8 address decoders like CD74AC138, with the address lines driven by GPIO and SPI_CS on one of the negative enable inputs. This way you will save GPIOs and the CS signals to the peripherals will be strapped with the SPI_CS signal.