Nothing bad will happen if you microwave cup noodles.
Although the cup noodles say not to microwave the cup noodles it's perfectly safe to do so.
Generally you're supposed to just boil some water and then pour the boiling water into the cup noodles.
However I have been microwaving cup noodles for over 10 years now and never had an issue doing so.
Just pour some water into the cup noodles and then place it in the microwave.
Then cook the cup noodles for around 2 to 3 minutes depending on your microwaves wattage.
Some microwaves cook faster than others so you have to adjust the time of your microwave to the wattage of your microwave for the cooking time.
For my low wattage microwave it takes around 3 minutes to cook the cup noodles.
You can also pour the cup noodles into a microwave safe bowl and cook them that way as well.
The reason the manufacture says you can't microwave the cup noodles is just as a safety guideline to protect them against lawsuits in the event you get sick or harmed from heating the cup noodles in the microwave.
But many people including myself cook cup noodles all the time in the microwave without any issues.
According to what others have said about cooking cup noodles in the microwave and as to the reason you shouldn't do so is.
Microwaving cup noodles can cause super-heating of the contents as well as can release chemicals from the foam.
Note, the cups are made from foam, not Styrofoam which is a trademarked material.
Most cup noodles direct you to heat water in a separate container in the microwave and then pour it in and close the lid.