If the ship still has a useful life measured in centuries, I think the economic incentive is still there.
But, regardless, compact-core ships aren't terribly more expensive, according to HMA. The Sylvester from TRO 3057R clocks in at merely 3.2 billion credits, for a 280,000 ton ship. That may still be 2.5 times the cost of a 274,000 ton Star Lord, but the Sylvester, despite wasting between 3,000 to 15,000 tons on surplus crew, heat sinks, and weaponry, still provides 73,000 tons of cargo. Yep, it's a lot more expensive, but it's also a lot more survivable, and much like real-world merchant ships, if you make it bigger, it becomes even more cost effective.
A Sylvester Plus, at 2,500,000 tons, crew to match, max armor (still standard), 20 DS collars (10x the basic Sylvester) has more than 800,000 tons of cargo space (about 11x that of the basic Sylvester) at only 18.6 billion c-bills, less than 6x the cost of a standard Sylvester. If you keep only the 2 DS collars from the original Sylvester, you get 822,000 tons cargo space for only 4.2 billion c-bills. Quite the steal, honestly. It'd take more than ten Behemoths to equal that cargo, they'd travel slower, you'd have to hire at least two ships to move them, and they'd cost you 6.3 billion c-bills, 50% more than your 2.5 million ton Sylvester Plus.
So, for bulk hauling, civilianized compact-core JumpShips have it all over JumpShip + Cargo DS.
