Hi,
the higher the signal frequency is, the better PCB enviroment one has to provide for proper operation.
I´d say it is somehow different.
For proper operation you always need a good layout. Because EMC doesn´t care about the frequency you use on your PCB.
The external signal may influence your operation even if you don´t have any clock on your PCB. Long messy wiring an a non solid GND plane will always be problematic.
That´s why a circuit maybe runs for a long time witout problems, then you neighbor buys a new handheld telephone and your circuit fails. ---EMC
But EMI, which means: "your PCB is acting like an RF transmitter" depend on clock frequency. But clock frequency is only one item of many.
Trace length, voltage levels, switching speed (rise time, fall time), how many lines are swtching at the same time, coupling to other wires, copper pour and, and, and... will have a lot of influence , too.
I often use a 48MHz Xtal with a short wire to an CPLD or FPGA then I use divided clocks (6MHz, 8MHz, 12MHz...) for my microcontrollers or periferals. I am a friend of only one XTAL clock and all others are generated from this clock. Especially when analog signals, ADC or DACs are on the PCB, this makes noise handling more easy.
Klaus
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added:
PLL and stablity:
What do you mean with "more stable":
* low jitter: this sometimes is not wanted. This causes sharp, high peaks at EMI measurement. Some add jitter to pass the EMI test. It is called "spread spectrum".
* more reliable: I don´t think that one solution is more reliable that the other (of your given two)
Klaus