Do you have an x-pen or something similar you can bring? You can then take breaks of maybe 1/2 an hour or so every few hours (3-4 hours if you can) and set up then pen to let them out. They can run around a bit. I would bring a tarp and blanket to put down to avoid them being on the grass, gravel which could have chemicals or other stuff you don't want them in contact with. The pen should be tall enough they won't try to jump out easily. This can be a good time to give them some food and water as well. I put hay in a tissue box so it isn't wasted when you only need a little bit.
You could use a cage instead of the pen, but a cage would be hard to set up quickly or would take up a bunch of space in the car.
You can also work on harness training them (both the rabbit and ferret). This can make it easier to get them out for a bit of exercise or at least some extra security in the pen so they can't escape. Make sure the harness is fitted right and they are used to it so they don't freak out. A tag with your phone number is also good just in case.
Use a bigger carrier, the Petmate medium size is good for a bonded pair where the rabbits are not too big. The large size would be good if they are bigger rabbits. The bigger size could be good for a long trip to give them some more space to move around. Try to find a used one as it is cheaper than a new one, if it is bigger that what you would want otherwise, you can sell it when you get there. You can also put a small litter box in the carrier as well if needed.
Since it is a long trip, take extra towels or whatever for the carriers. I would line the bottom with newspaper, then use an absorbent cloth (like the shamwow kind of thing), then a fleece blanket (you can find them at Dollarama or other dollar stores). Get 2 so you can change the bedding about 1/2 way. Also take a bag for the dirty stuff as it does smell.
If you did want to stay in a hotel, look for one that will take pets. A motel can be good as you can easily get them out of the car and into the room. Say you have a pet and if they ask you can say it is a cat since they would travel in a carrier and not make noise. Make sure to lay down something waterproof under a pen and clean up after yourself. If you want to let them run around, use the bathroom as it is easy to clean. Take your own cleaning supplies (paper towel, vinegar spray, small vacuum etc). It is easy enough to find hotels that allow pets. I have stayed in a hotel with 6 rabbits and didn't have a problem and I know people who have had more.
You can try putting something solid between the rabbits and ferret. You can't help the smell when they are in the same vehicle, but you can keep them from seeing each other.
