Stunted growth is a problem not completely understood, but the general consensus by biologists is that it is unhealthy.
Genetics may be implied here for long term effects of runted specimens. I have had several examples of such abnormal specimens where growth was limited to under 13 cm for most of these mutants, later resulting in death. I covered this under the species P. nattereri at the OPEFE web site. With normal specimens, stunted seems to be a condition that is temporary. However, I have not tested this to any degree and my own experience with piranhas raised in small containers for more than 5 years, usually resulted in the fish extending its length after a period of a few months. Not a hard fast rule, yet something to consider.