It all depends on how much 'handwavium' you like. If we were sticking to hard sci-fi then having fortresses guard the hyperspace lane points would definitely be a thing (of course that all goes boom once somebody discovers jump drives). However, if we stick to the Stellaris meta with starbases and planets with defense structures containing the FTL inhibitors, then it makes sense for the system defenses to be in the center of the system. Of course that also means that planets are vulnerable immediately afterwards instead of having their own orbital defenses, which sacrifices common sense in favor of the meta.