My 2 years boy had a pneumomediastinum in dec. our doctor ask us to pass a second x-ray, x-rays are not bad for him at this age?

Yes and No: Your doc weight the risks and benefits of the x-ray. Yes, radiations carry some cumulative risks of cancer, however there a bigger risk of complication from pneumomediatinum that may kill your boy now, especially if the dooctor doesn't have a clear reason why he has that. It will be safer to verify with x-ray if it's getting smaller or larger and determine what need to be done next.

It depends: There should be minimal risk in obtaining a second radiograph to determine if the pneumomediastinum has resolved. Chest CT scans have much more radiation than a chest radiograph. The link between complications of radiation usually involves much higher levels of radiation exposure, eg multiple CT scans.