I do not know the reason for the removal of Faction Ships from the Loyalty Point (LP) Store from this latest expansion update. My presumption is it was intended to increase manufacturing activity by using the Blue Print Copies (BPC) to make those Faction Ships. However, with the removal of Faction Ships from the LP Store from all Non-Player Character (NPC) Corporations and not replace it with BPC there is a limit on what NPC Corporations that the players can pursue in gathering LP from to receive those Faction Ships.
For example, before the update the Caldari Faction had 47 NPC Corporations that had Faction Ships within their LP Store. After the update, only 11 NPC Corporations have BPC on Faction Ships and the remainder 36 NPC Corporations have no replacement.
It is a bit of a grind to gather those LP for one NPC Corporation and have the incentive taken away without a recourse. Granted I could pursue Faction Warfare and quickly gather LP that way; however, what if I want to do Faction Warfare for Amarr but I want Faction Ships from Caldari and the location I operate in has Caldari NPC Corporations that I can do missions for to gather LP that at the time had Faction Ships within their LP Store? Am I now to quit Faction Warfare from Amarr, travel all the way to Caldari, join their Faction Warfare a day later (24 hour waiting period for those in unaligned corporations) to gather enough LP to purchase a Faction Ship BPC from their LP Store, quit Caldari Faction Warfare and travel all the way back to Amarr and then rejoin a day later?
Having BPC replace those Faction Ships that were taken out of LP Stores for the effected NPC Corporations would still retain the intended purpose of their removal, the production for those Faction Ships by players will still remain, and I am sure it will also increase the cost and value of those Faction Ships that are made.