Hi, 3mm VSD is really small. Small defects (less than 0.5 square cm) are quite common. With a small VSD, there is minimal shunting of blood and the pressure in the right ventricle remains normal.
Often, VSD's close spontaneously. This can happen within the first years of life of the newborn.
In small VSD, surgical repair is usually not recommended. However, long-term follow-up is required.
Also the PDA may close spontaneously. Your child's cardiologist will check periodically to see whether the PDA is closing on its own.
The medication is mainly needed for the PDA and its consequences, so yes she needs to take it (also the Lasix).
Surgery is probably not necessary now, and the future will show whether it is necessary then.
Discuss your safety concerns about the medication with the cardiologist. He/she will explain the benefit of it for your baby.