Not one in a thousand players use this tool – it’s not that it’s illegal ...

Does that mean 'even one in a thousand players doesn't use this tool (but maybe one in a milliion could use it)?

Hi LiJ

"Not one in a thousand" suggests that the number of players using the tool is "less than one per every thousand" players. The speaker may well be expressing a personal estimate, and may simply have used that wording to emphasize how very few players use the tool.
As LJapan has implied in his response, I would use "uses" in the original sentence, as well, as "one" is clearly singular.
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Yankeeless than one per every thousand"
Thanks, Amy.
 Philip's reply was promoted to an answer.
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Very important point! Thanks, Philip.