Apparently the forum doesn't like the word (when) unless I put it in brackets - grrr!
Designer mode has a lot of limitations. It is really used primarily to see what is happening rather than make major changes. New missiles will not be used because the NPRs don't know about them. When they design their own missiles, they keep track of the database ID of those missile types. Those IDs are them associated with the different classes that use them. When those classes run out they will attempt to reload with the appropriate missiles and may attempt to use other smaller missiles of nothing else is available. You would have to create the missiles, edit the database records for all missiles types then change all the class missile assignments. Equally, when you give them engine tech they won't use it. As part of the NPR research process, when they develop certain key techs they will update their designs. In this case, new designs will be created (when) they develop new engine tech. Without that trigger to force a design update, they won't use the new engine tech you gave them.
You could add extra ships or extra missiles if they are existing types and the NPR will use them. Adding things they don't 'know about' won't help. Equally, removing or changing things the NPR is expecting to be available will confuse them and cause bugs. This is why I don't advertise designer mode or recommend using it. It's just too easy to get yourself into trouble
