There are thousands reason to use hot runner system in injection molding but seems lacking of info not prefer the hot runner. As I know the hot runner can be considered as the extension of the barrel. In some cases it combines with the injection gate that it can inject to the part directly.
But have some suggestions of not using hot runner system:
. Cost saving for the prototype mould with low quality part production.
. Wall thickness is not extremely thin that it has filling issue.
. It can not be fit to the injection molding machine when hot runner is applied because of the manifold plate requires bigger mold size.
. Some material such as PVC not recommend.
. Difficult maintenance during the mass part production, not really difficult but comparing with the cold runner, it is a bit more difficult.