We stay at the Hojo regularly. Yes, you can park and check-in when you arrive, even if it is before official check-in time. If there isn't a room ready for you yet, you won't get room keys, but you will get a parking permit to put on your car's dashboard and Hojo will store your bags for you. They have a very large locked storeroom. This would be the safest option.
We have parked inside Mickey and Friends and also in the outside parking area next to the Mickey and Friends structure before with our possessions in the car. It's a hatchback. Basically, when going somewhere we accept the theory that our car could get broken into wherever we leave it, so we do our best to not make it look particularly attractive. We don't have any nice stereo equipment. We don't leave cords and chargers or electronics anywhere visible in the car. Yes, we might obviously have luggage in the back, but we neatly drape a blanket over the top of it all or spread some jackets across the top. We assume that a thief is probably looking for a vehicle that looks like it might offer a more obvious payoff. Might we get unlucky and still end up being the vehicle that gets broken into? Sure. We make sure not to leave anything in the car that we would find a hardship or major annoyance to lose, so, yep, that means if we have an iPad or laptop along on the trip it goes with us into the park that day. No purses or wallets or extra cash or IDs stashed under the seats, but we don't do that kind of thing anyway. Still, I don't believe that car break-ins at Mickey and Friends are rampant, and I don't spend my time in the parks worrying about it.
