In TPM Anakin simply flies his N-1 Starfighter into the hangar and accidentally sends a stray torpedo into the ship reactor core, obliterating the entire ship. I know the real reason, but what's the in-universe reason?
We know the early Trade Federation ships were converted cargo ships, could it be that there was some benefit to having your reactor in the inner hangar?
Wookieepedia does seem to hint that the entire outer ring was one gigantic hangar bay in the earlier models, so possibly they were too cheap to armor seal it off.
This also brings up the question of radiation. They can't let it contaminate cargo and random droids. So we'll have to assume the case it's in is only very light radiation shielding.