Should I worry about EMC when building..
ALWAYS. Any good engineer has EMC built in as a base level design criteria along with efficiency and cost. If you do not take it into account, you are setting yourself up for a bag of troubles later on.
Is it likely that it will pass the EMC test?
That really depends on the rest of the system. If the driver and the cables are all contained within a metal grounded case, it probably will. If it's a plastic box or the cables run outside the enclosure, it is much more likely to fail.
However, if you are designing properly, you will be endeavouring to reduce radiated electromagnetic noise within your system anyway. If you have any other electronics that are sensitive to noise, you really want to limit what you are generating in the first place so you don't trip yourself up.
Further EMC noise is cumulative. If this is part of a larger system, whatever noise this driver is creating gets added to the rest. As such it is important to take measures to ensure you contribute as little as possible.
Noise from the motor will depend on the quality of the driver as well as the chosen driving methods, but as a minimum you should be using shielded cables to the motor coils.