They can be profitable where there is volume. The assumption of said volume is where the issue is. Most entire worlds in The Imperium are lightly populated. Pop 7 is the population of England. To be profitable, it has to be cheaper to lift the goods into orbit in Planet A, transport them to Planet B, and transship them to the surface than it is to make the goods locally using the resources of the entire star system. Now, the entirety of the economics of the 57th century are made up out of thin air. So, it's entirely possible that this is the case and there's lots of trade. It's entirely possible that this isn't the case.
I will point out that Mongoose's Third Imperium material does assume these ships exist. There's some large ship stats scattered about. There's a discussion of a convoy of enormous trade ships in the description of Regina system in Secrets of the Ancients. What there isn't is floorplans for these ships or rules for the economics of superfreighter trade. Because these things don't matter for game play.
Do you really think there is a market for an "Element class Cruiser" box set of deckplans for a super freighter, such that it makes economic sense for Mongoose to publish one? Or rules for how that kind of trade works? Figure there's a lot of PC groups playing merchant bridge crew sailing back and forth between two large, safe star systems on a contracted schedule?
As far as claims of unprofitability some of that is analysis using the existing trade rules. Which are explicitly not designed to reflect the kinds of action that superfreighters are involved in. The trade and speculation rules are designed to cover tramp freighters that go to the smaller markets that the big guys don't go to. I can't remember if that disclaimer is outright stated in MgT2e's trade section. But it is in the functionally identical Cepheus Deluxe rules and covered in GURPS Far Trader and other older books. It has been the case since the first version of the rules came out (which, incidentally, didn't even allow ships that large to exist

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The Traveller rules are there to let you play Firefly, Pride of Chanur, The Polysotechnic League, the Millenium Falcon, and all the other tramp traders in sci fi fiction getting into adventures as they go from system to system scrounging up a living. The closest you get to covering superfreighters is GURPS Far Trader. And they basically just say: "They exist and they soak up almost all the trade in the big systems, so here's the scraps your players might have access to."