I guess if you're doing the same monologue as the last five people the examiners have seen it might be a disadvantage. But overall being a less/more popular monologue shouldn't make a difference so long as you score well in all the criteria.
Although I have to say, I'm more worried about the written exam then I am the monologue.
From experience - it's better to choose the more obscure monologues over the more "popular" ones. Because heaps of kids (even ones in our class) were burned by the fact they chose popular monologues and didn't provide great individual interpretations of it (e.g. Richard from Zig Zag Street).
My advice is to choose an absurdist/abstract monologue (or one that can be interpreted in that style); because it gives you freedom to do what you want with it - and you'll be more likely to come up with an individual/well-rewarded interpretation. I did the Arturo Ui monologue last year (as did my friend), and we were the only ones chosen for Top Class because the absurdist piece gave us license to be really creative.
Also - with the written exam; don't stress out about it. Just make sure you study up on your plays and your monologue. Apart from testing your knowledge of that - the rest is very "common sense" stuff (like how you'd run a rehearsal in order to achieve a particular goal).