Unsolved what links pressure wheels

This is a confusing question, looks like you are mixing up a few different unrelated issues. First of all, there is nothing that really links these together. Wheels, tires, hubcaps and brakes by themselves are only 'settings' rather than physical structures, they mean nothing by themselves and can't exist on their own. It's the wheeldata that receives these settings and generates the wheel, then resets some of them back to default so that a new wheel can be added without sharing the same settings (if this wasn't done, all wheels would share the same brake properties on the same vehicle for example). The only physical structure present in a wheel itself without wheeldata is 2 nodes linked by a beam, that act as center nodes for the wheel and define its location, which is modified on the suspension or hub side by nodeOffset. The pressureWheels section next to it doesn't create the wheel, it just sets up the parameters for it, similarly to what brakes, tires and hubcaps do, and it's the wheeldata that uses these parameters to create a wheel. When you understand this, it will be easier to get what causes your issues.

• Wheels, tires, hubcaps and possibly parts of brakes showing up incorrectly or not showing up at all depending if other wheels are fitted on the vehicle is the result of a different wheel's settings being loaded for your wheel's wheeldata instead of the ones you want. This happens because of the order the parts are loaded, and usually only affects the rear suspension, unless other sets of wheels are available on the vehicle. The cause is the wheeldata being loaded before the wheel settings, so it uses the settings of the front wheels (or any other wheels existing on the vehicle) instead. This also causes the rear brakes to not work at all, because the front wheeldata which cancels brake properties is loaded before the rear brakes that set them. The solution is to just be careful with the slot order (they are loaded in the order as they are defined in Jbeam). You need to make sure that the brakes, wheels and wheeldata are sub-parts of the same component (either all in the hubs or all in the suspension) in exactly this order: brakes -> wheels -> wheeldata.
• Wheels, tires and hubcaps not showing up at all no matter what: this happens for the front wheels only (or whatever wheels are loaded first on the vehicle), and the cause is actually almost the same, it is when wheeldata is loaded without any wheel settings for it at all because they all get loaded afterwards. Solution is the same as above but for the front suspension/hubs rather than the rear.
• Brakes not showing up until you equip their wheels: may be intentional design choice (when the node at the bottom of the hub reaches below the visual brake disc), may be because the vehicle is old and doesn't have support for it, or may be caused by an incomplete wheeldata definition or not having enough nodes on the wheel hub, or having the nodes too close to each other. If you have a VY node error in the console, then it's the latter. Otherwise it means it was not meant to have the brakes show up without wheels. The way this works is that brake discs or drums are created as wheels on the spindle side, and then are overwritten by the actual wheels when those are equipped.
• Brakes still working after you unequip them despite not showing up anymore: this only happens on the rear brakes, and can have several causes. For cars, the most common is an incomplete or missing pressureWheels section somewhere, either at the end of the rear suspension file or at the end of the front wheeldata file, that is supposed to reset the brake properties back to 0. On trucks and trailers with a tandem axle suspension, it's a common mistake that the slot order is mixed up, having front and rear brakes first and then wheels and wheeldata. The rear brakes should instead be after the front wheeldata and before the front wheels, as the front wheeldata is the thing that resets brake properties on these setups. This also causes the rear brakes to not work at all.

In conclusion, order your slots carefully, same reason why interior should ideally be towards the end.