I suppose you are using the ctrl-n in a search/replace to count the occurrences of "word" in the current file or in the text ?
In that case, you could use a particular tag or class to mark the words you want to ignore.
For exemple, with the tag <small>:
Pass this regex with a Negative Lookbehind:
(?<!<small>)marked-word
on the text:
this marked-word will be counted, but this <small>marked-word</small> won't
Ctrl-n will give 1
Of course, you could use a <span class="ignored"> as well, with the convenient style in the css (a snippet can be used to insert it easily)
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