Yes, for the initial import, all packages that had evidence of being installed via Package Control are counted. There is no tracking of packages being disabled.
It is still pretty early from a statistics point of view since it has been less than 24 hours, however I would imagine sampling almost 1000 users already would give a general idea of the install percentages. I've been keeping an eye on it since yesterday and most of the percentages have stayed the same since around 100-200 users had submitted.
One possible reason for the low number for many plugins may be due to the fact that their readme files actively encourage using git, or manually downloading the package instead of using Package Control. I know that many of the plugins with high numbers have been promoted in popular blogs that also encourage using Package Control.