well,imagine it like this.The purpose of warp gates is immediate travel with no charge time over a much longer distance. Building a non-drone combat ship without a JD is like building a shuttle without thrusters.
Does this mean AI are going to be using warp gates, though?
Only the 3 main factions (Trade guild,Scavs,and a yet to be announced one) will be everywhere in the universe,with the jumpdrives,top of the line weapons,etc.
But the minor factions (the ones we players will create ships for) will be local maybe,underdeveloped somewhere,advanced elsewhere.
So its only logical some might not have JD yet