Let me answer your questions in the order you posted them. The following units are used in the calculations:
1. The unit of charge is electric unit (e), which is the charge of an electron.
2. The y axis of the pI calculation is the charge of the actual microspecies, so it is e as well.
3. The unit of mol. refractivity is 106·[m3·mol-1].
4. For the unit of the orbital electronegativity see the following post:
5. The unit of the Hückel calculation is beta, see the post above.
To know what the donor/acceptor plots are please read the HBDA manual you linked. The definition is in the introduction part.
The numbers that the Orbital El. plugin calculates are the atomic contributions of the orbital electronegativity. The explanation is in the linked manual. For the explanation of the red/blue numbers in the Hückel Analysis Plugin please read the Options part of the manual. The meaning of these numbers are explained there.