“But kamma beeja are stored in the mano loka of each being. The mind is connected with the mano loka. Why is dhamma (e.g. kamma beeja) not directly sensed by the mind or hadaya vatthu?”
For the same reason that sound is detected through the ears. Mana indriya in the brain can suffer damage (or degrade as one gets old) and one can have memory problems. Alzeimers is possibly due to mana indriya being degraded. This is why the physical body is called “vipaka kaya”. It is capable of imparting kamma vipaka in so many ways.
“How can an arupa brahma sense dhamma without mana indriya?”
It is likely that even rupavacara brahmas do not have a mane indriya and the hadaya vatthu can directly detect signals (dhamma) from the mano loka. In fact, for human gandhabbas it is the same: They don’t have eyes but can see, don’t have ears but can hear. They just cannot touch and taste. Regarding smell, though, it seems that gandhabbas can inhale aroma. I am not sure what that mechanism is. We will never be able to figure out all the finer details, unless somewhere in the Tipitaka.