If it's part of the story, ie it adds something to actual content, then it is part of the word count.
If it's just references, then it's not part of the word count.
But a disclaimer can mean a few things. Ultimately is depends on the referee's interpretation.
For example:
Disclaimer: Names have been changed for legal reasons.
sounds more like a reference to me, and therefore no word cound penalty.
but...
*Disclaimer: Field goals were worth 2 points prior to 1971.
is adding to the story and should be included in the essay.
I stress that this is just the way I see it and others may differing opinions.
Like I said, it's one area where you have to rely on the referee's ruling.
It doesnt come up very often.