Smoking anything is going to give you some lung problems if you do it for long enough. The fact that you inhale really deaply with bongs will make the smoke go right to the end of those little sacks in your lungs (cant remember the exact name) more than it would with a pipe or joint. I have took some big bong hits though and im still good.

I always accept that by smoking it is going to have some affect on my health.