Not 100% sure i understand your problem correctly, but the hierarchy of PI AF does have it's limitations. While there are ways to work around or remodel to put the information in the model, the way you structure the model also influences the possibilities you have to pull the data out of that AF model.
So to be of better help, i think we need some more info on the type of problem you need to solve. So what kind of data model, and what kind of data do you need to get out of that model?
You can create all equipment in one hierarchy and reference the same using substitution parameters. You can align your hierarchy based on equipment and reference in another subsystems. I would suggest having subsystem wise equipment and use reference in other assets.
Create a Parent-Child element reference for Equipment under Asset B like such. Notice the small little arrow which indicates that it is a reference.
When you edit the Equipment element under Asset A, the changes will automatically be reflected in the Equipment element under Asset B. Because they are the same thing. Similarly, when you edit the Equipment element under Asset B, the changes will also be reflected in the Equipment element under Asset A.
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In its very simple form, PI AF provides ways to create a shortcut to your element. This is a 'Weak Reference' element.
More details can be found in below YouTube link:
Edit: Eugene was faster than me by 1 minute... but i'll leave a YouTube link for your reference.