I have a project that is fairly old (maybe 18 month to two years) that is just shy of 70,000 words and takes at least a minute on a high-end gaming system to generate a project word count. (Long enough to start a pot of coffee and come back to find it hasn’t finished.) For comparison a newer project that I manipulated to be 69,000 words (I duplicated a set of chapters with 23,000 words until it reached the needed count) takes low single-digit seconds.
This feels more like an issue with a corrupt file rather than something with Scrivener itself.