But that's the catch, they are showing up in the Spirit part of the reading. I do believe that problems in the spirit and heart can manifest in the mental and physical, and in a reading would look at the interactions.
What sorts of illness are associated with the spirit? What recommendations/guidance does one give? If the source of the illness is in the spirit, then treating the body or mind will not cure the problem. Two examples, one with the nine and the other with the three.
1st example: mind/Emperor, body/2swords, spirit/9swords, heart/Devil
This one clearly shows an imbalance in the heart and spirit, with the mind clear but inflexible, and the body neglected with a host of petty ailments.
2nd example: mind/Emperor, body/Prince of swords, spirit/3swords
In this one, the imbalance is tilted towards the mind, with the body and the spirit being neglected or abused.
In both, there is a connection between body and spirit. Now I can see with the second case, that the problem may originate in the mind and through treating the mind through counseling should alleviate the imbalance indicated by the swords.