I tried to make similar script, and the result are the same, only 607 files indeed. And I even checked sizes of the all unpacked files, and it was close to the original packed WAD file (51.4 MB).
Interesting! I wonder what the missing link is here - I know for certain there are more than 607 pieces of data, but perhaps they're not stored individually like that? I think my next step is to dig into one of the utilities that found images/models/etc and see how they're operating.
Update: I just tried to open one of the unpacked files in jPSXdec, and sure enough, there are images in there. Looks like they're just grouped into the various .DATs? Which is exciting news! So it seems like it is being correctly unpacked after all, and my assumptions were wrong.