Well, VOY's S5 episode "Extreme Risk" showed the design and construction of the Delta Flyer, and it was rebuilt at the start of S7 (lost in the S6 finale). This solves the riddle of Voyager's endless shuttles - they rebuild them when lost. Now, here's the real question. Presumably, Voyager has at least 2 of those small speedboat-looking shuttles, 2 of the boxy shuttles, the Delta Flyer, and Neelix's shuttle - the Baxial. Whenever we see the inside of the shuttlebay, it's always empty or just one shuttle. Where did they all go?