is it possible to compute critical points and bond paths only for selected pairs of atoms? Out of more than 400 BCps only 5 are of interest for me, and looking for those every time for multiple structures is a pain.

You can select "1 Search CPs from a given starting point", then input index of two atoms, then midpoint of these two atoms will be used as starting point for searching CPs. I think this mode should be appropriate for your case.

I'd like to ask a short question about your Multiwfn program. I computed a set of critical points and bond paths, according to the QTAIM theory. Is there a simple way to determine which critical points belong to which bond (that is in-between which atoms such CP is located)? When saving a detailed data into the CPprop.txt this information if not present, doing it by hand or using the Multiwfn visualiser is very troublesome since the molecule is very large

Here I take water as an example.
We first locate its CPs and generate bond paths, then go to "-5 Modify or print detail or export paths, or calculate property along a path", select "1 Print summary of paths", you will see

#    1     CP:    4 (3,-1) ---> CP:    2 (3,-3)   Length:  1.41000
#    2     CP:    4 (3,-1) ---> CP:    1 (3,-3)   Length:  0.27000
#    3     CP:    5 (3,-1) ---> CP:    3 (3,-3)   Length:  0.27000
#    4     CP:    5 (3,-1) ---> CP:    2 (3,-3)   Length:  1.41000

It is shown that CP4 links CP1 and CP2 via bond path #1 and #2. Then return to main menu of topology analysis and select option 0, you will see below information on console window

Summary of found CPs:
  Index               XYZ Coordinate (Bohr)               Type
     1    -0.000000000    -1.381088249    -0.863018600   (3,-3)  Nuc:    3(H )
     2    -0.000000000    -0.000000000     0.225448153   (3,-3)  Nuc:    1(O )
     3     0.000000000     1.381088249    -0.863018600   (3,-3)  Nuc:    2(H )
     4    -0.000000000    -1.139059094    -0.680319212   (3,-1)
     5     0.000000000     1.139059094    -0.680319212   (3,-1)

Clearly, CP1 and CP2 correspond to H3 and O1, respecitvely. Thus CP4 is bond critical point between H3 and O1.