Thanks for your anwers - I found this information elsewhere
If using MAME as NES emulator it looks inside the zip, goes to the Hash file and compares the checksums and uses the data within the Hash to figure out how to properly run the game with the PRG, CHR, etc, components. Basically, the HASH replicates the header data for NES format. For MAME it makes sense they do it that way since fits there overall model of how dump ROMs, but does make sharing MAME ROM sets with non-MAME emulators problematic (or vice versa really).
if this is correct MAME should find every information in the zip file without converting anything (right?) 
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