Is NGC 6-digit holder worth more than 7-digit?

No, the six-digit was graded before the seventh digit came around. (serial number 999999 was graded just before 1000000)

This is like the old(er) ANACS holders bringing higher premiums than the newer (blue and gold labels) holders. Being said that their grading standards were more stringent back in the day compared to today could warrant higher prices realized. Then again it may be who was bidding on the items in question as far as strike, eye-appeal, etc... goes.

I can't say I buy into a coin being worth more in an older holder, yes the TPGs were tougher on grades in the earlier days but almost anything worth being cracked out already has been. A coin is worth, what it's worth, the holder shouldn't play into the value, at least with the top tier TPGs, NGC and PCGS, ANACS and ICG seem to have always brought a lower price, but if the coin is accurately graded there should be no issue.