It is possible that you are looking at collapsed versions of the lists.  If you have only one entry under missile ships, for example, try to click on the little carat mark to the right of the ship list name.  It should expand the list to show you resource dependent ships and other variations.  If you favor the non resource version, it will be there at the top of the whole shipyard list.

Unfortunately that is not the case. . . the lists are fully expanded and just don't show the ships that don't require resources.

Ok I'm confused the shipyard has a plethoria of organizing features this should not be a problem in the shipyard. I looked at the statbase it doesn't have anything along any lines of what your talking about. both the ship designer and the shipyard sounds more along the lines of what your talking about. Except the sorting has for special ships, and a lot of pther ways to sort. I need clarification to understand this. Are you usinbg the current version.

If I have researched Weapons Systems, then the only non resource weapon available is Lasers.  If I research any individual weapons tech, it adds non-resource weapons ships of that type to the list for that type.  If your game is not doing that, then you should consider submitting a ticket to Stardock and let them help you.