An atrial septal defect is a condition in which an opening is present which allows communication between the two upper chambers (atria) of the heart. Animals are born with this condition and depending upon the size of the opening, it may cause no problems or it may progress and lead to right-sided heart failure. In the majority of cases, since pressures are greater on the left side of the heart, the blood is shunted from the left atrium to the right atrium. This leads to volume overload of the right side of the heart and subsequent enlargement of the right atrium and right ventricle. When the right side of the heart is overloaded, this leads to pulmonary edema (fluid within the lungs) and ascites (fluid accumulation within the belly as a result of increased pressures within the large vessels bringing blood from the abdomen back to the heart). Pleural effusion, which your cat apparently has, is fluid accumulation within the chest cavity but outside the lungs. This is a less common finding with right sided congestive heart failure, but it can occur.
Removing the fluid from around the lungs is only palliative- it makes your cat more comfortable so that he can breathe more easily. It also allows the veterinarian to examine the fluid to determine if it is consistent with fluid loss secondary to increased pressures, or if there is another cause such as tumor, infection, or rupture/malfunction of lymphatic ducts.
You mentioned 4 congenital heart defects. The only situation I'm aware of with 4 simulataneous defects is Tetralogy of Fallot, but in this condition the hole is between the ventricles, not between the atria. Did your vet mention what the other defects were?