You are asking for best, I can give an answer (how I solved it), but cant say if it is the 'best' way (in your environment), I had the Problem to collect inventory data of many thousend PCs (no not NSA - kidding)
my soultion was:
One table per PC (File for you?)
Table File: one row per file, PK FILE_ID
Table File_data one row per column in file, PK FILE_ID, ATTR_ID, ATTR_NAME, ATTR_VALUE, (ATTR_TYPE)
The Table File_data, was - somehow - big (>1e6 lines) but the DB handled that fast
HTH
EDIT:
I was pretty short in my anwser, lately; I want to put some additional information to my (and still working) solution:
the table 'per info source' has more than the two fields PK, FILE_ID
ie. ISOURCE, ITYPE
, where ISOURCE and ITYPE dscribe from where (I had many sources) and what basic Information type it is / was. This helps to get a structure into queries. I did not need to include data from 'switches' or 'monitors', when searching for USB divices (edit: to day probably: yes)
the attributes table had more fields, too. I mention here the both fileds: ISOURCE, ITYPE
, yes, the same as above, but a slightly different meaning, the same idea behind
What you would have to put into these fields, depends definitely on your data.
I am sure, that if you take a closer look, what information you have to collect, you will find some 'KEY Values' for that