Electronic – Should I avoid a switching frequency close to the target SPI or CAN frequency

As far as I know this would be better due to the EMI and SI issues, it's easier to get rid off one frequency than multiple of them and their harmonics, products etc.

This is a false premise. EMI regulations limit the emissions on a frequency-by-frequency basis. If you have two sources in your system at the same frequency, their outputs can add, giving higher emissions at that frequency. If they're at different frequencies, they are effectively independent for purposes of emissions.

It's a general rule in EMI design that the best solution is to reduce your sources of emissions, rather than generate signals and then try to block them. So I'd say for EMI purposes, you're better off using different frequencies for your different switching regulators.

4-20ns rise time is pretty slow - each nanosecond is about 15cm at PCB trace speeds. Various rules of thumb exist - Howard Johnson proposes that if the length of your interconnect is < 1/6 of the risetime, you can treat it as a lumped circuit and neglect most of the signal integrity problems that rear their heads in longer circuits.

For you, 4ns is 60cm, so if your wires are shorter than 10cm, don't worry about it.

Regarding mitigations, without access to a simulator, the easy things to do are:

• Series terminate the serial-clock line, some value between 27 and 47 ohms is usual.
• Ensure that there is a ground return next to each signalling wire in the ribbon/flex cable. If you can't do that, ensure that the clock line is at least next to a ground line.