Where do worlds with poor atmosphere get their food, water and air?

I think you're right, I'm not sure there are many alternatives to this for air, or even water. But it would need to be done on an industrial scale with a population of even a few hundred, let alone thousands. Not sure how they'll get on with this on Mars. So I guess the first thing colonists drop on a planet is a massive electrolysis plant.
You might want to read Red Mars from Kim Stanley Robinson. Part of the book describes the life of the 100 first colonists on Mars.
So there are a lot of technical ways - but nobody can really tell you how "practical" they are going to be simply because we have no way of knowing costs associated with them. Plus throw in the total unknowns of life support tech/sciences in the 52nd century. Humans can be awful weird and resourceful, so just about anything is possible. Don't limit yourself to just the practical.
This is an important point. There are many different situations, and access to advanced technologies, some of which you can find in the rules, but others related technologies have to exist logically, but the rules can't cover everything. We can assume that within Traveller tech levels, independent space habitats are viable with resources found in pretty much any solar system. Whether it makes more economic sense for them to import food farmed on planets, or to grow it themselves will depend on how far from those planets they are, and what the transportation options are, on the supply side. On the demand side, it will depend on how easy it is to grow their own. The higher the tech, and the greater the distance, the more they will grow themselves (if the habitat is big enough). On the other hand, if there is a space habitat that just happens to be a stopover on major grain shipping route between an high production ag world, and a super high population hell world, you can bet they just get their food by buying a little bit of what is being shipped through anyways for themselves. Large scale shipping operations bring the cost down greatly, the way the rules are set up. Smaller scale shipping is more expensive per unit of cargo, so lower pops involved and smaller cargo sizes will make local production more expensive.

It also doesn't need to be just one solution - if possible food is sourced from multiple places. High tech wealthy habitats may be making their own food and buying it from many sources for variety, and high value items might be shipped from very far away.