i mean does phenix differentiate in refinment between SN, SN2+ and SN4+?

In the phenix.refine log file look for this section:

============================== Scattering factors =============================

----------X-ray scattering dictionary----------

Number of scattering types: 4

Type Number sf(0) Gaussians

Zn2+ 1 27.88 1

O 20 7.97 2

N 12 6.97 2

C 33 5.97 2

sf(0) = scattering factor at diffraction angle 0.

The "Type" is exact including charge. The label is one of the entries from Int Tab Vol C Tab. 6.1.1.4. For SN this is your list above (SN, SN2+, SN4+).

Ralf