Well, I don't think this "unprecedented" score could be low. Let's break this down and examine the word unprecedented to see what exactly this could mean.
Main Entry: un·prec·e·dent·ed
Pronunciation: "&n-'pre-s&-"den-t&d
Function: adjective
Date: 1623
: having no precedent : NOVEL, UNEXAMPLED
Hmmm. No precedent... Let's look up precedent.
Main Entry: 1pre·ce·dent
Pronunciation: pri-'sE-d&nt, 'pre-s&-d&nt
Function: adjective
Etymology: Middle English, from Middle French, from Latin praecedent-, praecedens, present participle of praecedere
Date: 15th century
: prior in time, order, arrangement, or significance
Prior in time, order, arrangement, or significance, and prior is very close to priority and related to prime. This score will have no precedence, however. It has no order or arrangement. If it had no significance, we wouldn't be discussing this. This would have to be a different kind of score, a positive one most likely.
Let's examine some synonyms to re-examine the tone of this word. So far, I don't think unprecedented can carry a negative tone. Novel and unexampled may give us an idea.
Main Entry: 1nov·el
Pronunciation: 'nä-v&l
Function: adjective
Etymology: Middle English, from Middle French, new, from Latin novellus, from diminutive of novus new -- more at NEW
Date: 15th century
1 : new and not resembling something formerly known or used
2 : original or striking especially in conception or style <a novel scheme to collect money>
Main Entry: un·ex·am·pled
Pronunciation: "&n-ig-'zam-p&ld
Function: adjective
Date: 1610
: having no example or parallel
Novel means new and unlike anything else. It's original or striking especially in conception. This sounds very positive. A novel idea would be to create a yoke to let an ox pull a plow instead of man dragging the plow himself. A novel idea would not be, "Hey Jimmy, look at this! I can get the bull to produce milk, too!" Not the best example of a bad idea, but if this unprecedented score was going to be negative, that would mean Legend of Zelda: The Wind Waker would not have been a novel creation.
Unexampled. It has no example or parallel. Does this mean the score is peerless? Is Wind Waker peerless? I believe so. No other game achieves what it does. There is nothing like it. The game plays like a movie with as much emotion and creativity from its characters as we've seen from some of the best movies ever produced. It will be a true timeless classic to those who recognize it.
Unprecedented obviously carries a positive tone if correctly employed. Synonym NOVEL is definitely favorable. Given EGM's record of being a reliable video game magazine, I seriously doubt they want to risk their reputation and business by straying from the pack, so to speak. EGM has a goal in running their production. That goal is to gain respectability even from audiences they may not neccesarily take a personal liking toward. They have more to lose by insulting a portion of their consumers. If The Legend of Zelda: The Wind Waker is receiving positive scores, it would make more sense that they be bold and match someone like Famitsu with top scores and even a new award rather than to be ultra critical and give an inaccurate review. Their credibility is their actual product. In the information world, credibility is all a true publication has. It's almost like a stock price. The higher your credibility is with your market, the more valuable you are.
It's not likely EGM will take a personal stance toward Wind Waker and sling mud. They will probably give it very high artistic scores and maybe even a new type of award for originality, quality, and fun. If anything, this would put Wind Waker off to the side by itself away from Grand Theft Auto, Metal Gear Solid, and Final Fantasy. It'd be like segregation in a way.
Honestly, there's not much to expect from a rumor like this, and I really wouldn't make too much of it. No matter what score EGM gives it, it won't likely stray from the norm unless they have something somewhat positive to say in the process. They have invested interests that rely on their words. What all can they say?