Weep holes vent any permeate which passes through the liner, either through liner defects or by diffusion through an intact liner (halogens tend to do this). Permeate might otherwise accumulate in the space between liner and containment shell and potentially cause the liner to collapse inward.
In corrosive services, especially when the pipe is insulated, a threaded half coupling is welded around the weep hole and a "sacrificial" threaded nipple is installed. Corrosion due to permeating corrosives is usually worst where the permeate contacts the moist atmosphere. Rather than corroding the pressure-containing shell from the outside inward leading to a loss of containmet, the permeate corrodes the nipple over time. You can remove them and replace as needed.
Some systems use rifled bore pipe and vent devices located between the face of the flange and the face of the liner to accomplish the same effect.
Systems with bonded liners (i.e. spray-applied) do not need vent holes as liner separation is not credible.