I think that when Voyager departed Mars that the Areoshuttle was, for some reason, unavailable. And what the Voyager actually had was basically a "plug," to occupy that space, and make Voyager's underside aerodynamic in case she had to enter a atmosphere.
Alternatively, again the shuttle was missing, and what we were seeing was the sliding hatch/hatches that closed when the shuttle was on a mission, the hatch would make it so the Voyager could land without the shuttle in place.
Non-canon sources from a Star Trek Magazine suggested that Voyager did have the Aeroshuttle, but that it was undergoing an overhaul at the time the ship was initially lost in the Badlands.
I'm tempted to agree with the "plug" theory, although the features on the underside look oddly like maneuvering thrusters...
As for the sliding cover, I don't think one was planned. According to the following draft animation that the producers pitched for the show, the Aeroshuttle simply pops out and flies off leaving a cartoon cutout:
So, what could I possibly put in its place?
- Plain hull plating?
- Additional sensors?
- Additional phaser strip / torpedo turret?
- Lower observation lounge window?