It hardly makes them look like fools. Was Ford a fool for his hand cranked car engine? They were designed to hold stuff not be hyper optimized.
There are also many reasons one could justify only fitting in the new ships. For example removing most of the structure between the canisters would make the whole assembly very weak which would require much stronger structure around the outside. Hence the new ship might need reinforced hull in that area to withstand the stresses.
I'm sorry but that's a terrible comparison.
The model T arrived in 1908 and it took exactly 4 years for Cadillac to come up with the electric starter.
A slightly better example might be related to shipping itself, where cargo ships used to take crates and sacks of any size in their holds.
It was only back in the 1950s, after 200 years of industrialised freight transport, that we came up with standardised shipping containers.
Even so, shipping containers didn't really allow ships to carry more stuff.
They just made it easier to load that stuff.
We know what a standard 1t cargo canister looks like in ED and we know that ships like the Anaconda have been around for nearly 500 years.
It seems highly unlikely that a society capable of building spaceships that haven't been rendered obsolete for 500 years somehow overlooked the best way of stacking cargo during all that time.
... unless they're fools.
Above all it's just a game and the devs can do what they wish.
That's the correct answer.
Honestly, I don't think it's a big deal to add enhanced cargo racks but it's best to just accept it rather than trying to justify it in real-world terms.