1 This can be confirmed by performing AIM basin analysis via main function 17, please check the "Special case: Basin analysis when pseudoatoms are presented" part in Section 4.17.1 of the latest version of Multiwfn manual, there are example and relevant discussions.

In addition, you can also perform AIM topology analysis using main function 2. For example, the analysis result for "examples\Li6.fch" is shown below. The CP7, CP8 and CP10 do not correspond to any nucleus and thus they can be regarded as NNA.

Summary of found CPs:
  Index               XYZ Coordinate (Bohr)               Type
     1    -0.000000000    -5.659739181    -3.267656873   (3,-3)  Nuc:    4(Li)
     2    -0.000000000    -2.845928989     1.643747599   (3,-3)  Nuc:    3(Li)
     3     0.000000000    -0.000000000     6.534368883   (3,-3)  Nuc:    6(Li)
     4    -0.000000000     0.000000000    -3.286550347   (3,-3)  Nuc:    1(Li)
     5     0.000000000     2.845928989     1.643747599   (3,-3)  Nuc:    2(Li)
     6     0.000000000     5.659739181    -3.267656873   (3,-3)  Nuc:    5(Li)
     7    -0.000000000    -3.445160677    -1.989385399   (3,-3)  Nuc:   Unknown
     8     0.000000000    -0.000000000     3.977764187   (3,-3)  Nuc:   Unknown
     9    -0.000000000    -0.000000000    -0.000863492   (3,+1)
    10     0.000000000     3.445160677    -1.989385399   (3,-3)  Nuc:   Unknown

2 In the basin analysis module, the NNA basins are treated exactly the same as usual basins. Therefore, you can get the number of electrons in the NNA basin by choosing "2 Integrate real space functions in the basins", and get localization index by choosing "4 Calculate localization index and delocalization index for the basins".

3 In main function 2, perform AIM topology analysis to locate CPs first, then use option 0 to check the CP index corresponding to the NNA, and then select option 7 to check properties of this CP.

4 Please check the ELF basin analysis example in Section 4.17.2 of Multiwfn manual.