These "stink" pipes as you call them are in fact the vents for your plumbing system. One of two things is happening now. First, the vents are not completely blocked and you are filling your attic with sewer gas. Depending on what type of sewer you have, you can be building up methane gas in your attic and that is flammable. Second possibility is the vents are completely clogged and your fixtures are not venting properly. This can cause a slow toilet flush or worse; when you flush the toilet, it sucks the water out of the trap of a nearby sink to vent and then lets sewer gas into your house.
Since you did not describe either slow toilets or sewer gas into your house, I would guess you are filling your attic with sewer gas. Bottom line, those vents are there for a reason - have them vented back up through the roof at least 6 inches (or whatever local codes prescribe) and flashed properly. Your roofer should know better. There is no way the building department will pass the roof inspection if they know vents have been cut off.