I don't see the problem. The system that reads those floppies is probably very deeply integrated into the ship and does it's job very well. At the same time, being able to give it something like a USB instead will update the actually troublesome part (floppy drives) while keeping the part that does it's job correctly untouched.
I do think that USB would not be a good choice, considering how frequently they've been implicated in malicious actions. I mean, USB as the bus would be fine, but, it should use a more esoteric connector.
Yeah. I'd go with something like USB over D-Sub (both for practicality and the word play). It's a nice sturdy connector and would be easy to service, etc due to the large pin size.