The game received an update a few days ago, and they reset the leaderboards.
I hadn't realised but maybe they reset the achievements too. When I say reset, what they did is empty the leaderboards whilst keeping them stored offline, then they're repopulating them on an account by account basis as accounts play the game again (or for the first time) post-update. This was to get rid of hackers, which sort of worked but I see there are new hackers.
Anyway, before the update the leaderboards indeed were: - 46,143 for Adventure Mode 1. - 972 for one of the Bonus Levels. - 14,957 for Deadline. - 13,859 for King. - 17,635 for Evolved. - 18,474 for Pacifism. - 15,624 for Waves.
The results of your calculations seem closer to the players who've logged in in the last two weeks, or since the update 3 days ago, to be precise. http://steamcharts.com/app/310790 As you can see there's been an uptake in activity since the update.
To explain your 44 players having done the Nufo Flow achievement, for instance, I looked at the leaderboards and like you say 44 people have done it, but that is only of the people who've played the game in the past three days. Using the 0.7% you've simply calculated that 6285 players have opened the game in that short time. In fact though, I suspect the people who've played recently have completed the game's achievements at an inflated rate as compared to the average, so you can't really tell much at all from that.
As of this moment there are 2,500 players on the second level of Adventure mode's leaderboards.
By the way, to anyone still reading this Geometry Wars 3: Dimensions Evolved is a great game. They now have all the Classic levels except Sequence, as well as the 50 levels in Adventure mode, 40 more in the new Ultimate mode (including a new type called Scorpion), and Hardcore variations on 20 of those 90 levels that have you play without the use of a drone. Local co op and online multiplayer modes as well, though sadly no online co op as yet. The developers seem pretty motivated to continue improving the game though. I highly recommend it to anyone who's played Geometry Wars and enjoyed it. They also fixed Pacifism with the recent update.
Note: currently the Classic modes do not support local co op like they did in Geometry Wars 2.