EMC Design Precaution
1.- Yes, sure. You always must attend the EMC performance of your electronics design.

EMC or Signal Integrity, we are talking about the same. Although probably It's a hobbyist-project and you won't need to pass an emission or immunity EMC test in a EMC Lab but EMC is also the noise, the crosstalk or ground bounce and this could be a problem inside your project.  

So, yes. For emission you can check: (only a summary)


Raise/Fall Time in high speed signals.
Layout of high speed. (Changes of layers, loop current...)
Possible antennas. (Your connector and your cables could work as an antennas)


2.- It would better if you explain us more about your circuit. 

I suppose there is a component that works as a switch. The out of this component we can call it "switch node". In this node the voltage is

$$V = L (di/dt) $$

; V is voltage, L the inductance of the node, i is the current, and $$di/dt$$ is the rise time (or fall time) of change.

This parameter is really important!

Maybe you can:


Decrease the rise time. (Could it work slower?)
Decrease the voltage (Could you use a lower voltage?)
Decrease the inductance in your switch node. 
Include a snubber (a circuit for absorb the voltage peak).


3.- This question is the similar to 2 isn't it?