At least its only these few balance issues to deal with.
All in all the orignal FL weapons are balanced, but with anyone being able to easily get nomad and codename weapons with little, if any, difficulties they don't get used much.
Plus with all the other weapons added there isn't as much varity in fighter loadouts because everyone seems to focus on PvP more then fighting NPCs, as an example: you don't need to equip tizonas or coladas when fighting NPCs.
As for the capships, some look like FL ships, others don't, but they are getting used, so you don't see factions using as many 'questionable' capships anymore.