Personally, I'd say the primary use-case for these not being hard-caps is specifically the case of "when you're docked at a market". Instead of needing to add a bunch of special corner case code, the game just displays that you're over-cap on crew/cargo/fuel if you put a bunch of ships into storage, and you can resolve that by storing stuff or taking (presumably other) ships out of storage, or buying new ships, or selling things, or etc.
Or the case where there's a cargo mission for 800 units of whatever, and I currently have 780 space free; I can just take the mission, then maybe temporarily add expanded cargo hold to a combat ship, or sell off 20 units of something, or even just buy another ship.