As said above there is a blueprint for each fighter that decides for you what will be on them. This might change in the next patch, but currently each fighter type uses a specific weapon type. For example Interceptors will only use beams, so if you unlock them and research any other type of weapons those won't impact them. So you're not going to suddenly have them using kinetics or missiles, even if these are your best weapons. Or at least that's how it used to work. In Crusade they made it so that they would only use the basic beam weapon. So researching better beams makes no difference to Interceptors.
Defences are a bit less restricted as they use "Bestdefence", which seems to use your most advanced defence tech (not sure how it decides if you have techs on the same level). So you could change your fighters from using armour to point defence if you research PD far enough that the AI decides it is now your best defence.