All the files I have are *.nes files since NES game normally contains only one file and is relatively small. I don't know of NES header info before so I did a few experiments.

I use nestopia's edit iNES header feature to change Battle City (1985-09-09)(Namco)(Jp).nes header info of NTSC to PAL and save it, then compare the saved to the original, only one byte was changed. So I think the nes file does have header info.

Then I calculated the md5 of Battle City (1985-09-09)(Namco)(Jp).nes and compare it to the game info of Tosec's dat:
game (
name "Battle City (1985-09-09)(Namco)(Jp)"
description "Battle City (1985-09-09)(Namco)(Jp)"
rom ( name "Battle City (1985-09-09)(Namco)(Jp).nes" size 24592 crc f599a07e md5 cd4fe2e78df0696dbe652f02c19541a1 )
)
Identical. The dat is built with header info. So the problem should be neither in the nes file nor the dat file.

Then I zipped the Battle City (1985-09-09)(Namco)(Jp).nes to Battle City (1985-09-09)(Namco)(Jp).zip. Scan shows the number of missing files decreases by one. So it seems that clrmamepro does not check any file out of zip to find missing roms.