Yes. IB Extended Essay markers are quite strict indeed and if they suspect your essay could be slightly over the limit, then they are instructed to count. And so, if you even have 3,999 words, that rather suspicious and it may provoke the examiner to count (and you never know if they will miscount thus harming your mark- losing 3 marks out of a maximum of 35 (or 36 :?)).
My word count was 3,919 in the end. I think thats a good area to be at. But remember you can always include extra info in your footnotes, diagrams don't count, and also the appendices (though again, examiners are not required to read appendices so that could be risky).
For all i know, you can take a bit of your text and put it in a table (photoshop it to make it look like some decent source extract) and just label it as a source, in order to cut down on the word limit. Even though the word limit is 4000, many essays will approach 30 pages in length. Another word of advice: make sure you number your pages. You actually lose marks if you don't. And that is truly a waste...