Last Active is updated when a user visits the board for the first time that day.
If a user hasn't visited the board since we started tracking Last Active (6.6?), or hasn't visited since registering (more accurately, hasn't made another pageview since registering and getting the registration confirmation screen), then the Last Active field will be blank.
As you've noticed, blank Last Active dates can cause some odd search results when searching for the field.
And your guess is likely correct, based on when you upgraded to the recent versions. If you've been using 6.6/6.7 for a few months, then the count is likely accurate.
It's not abnormal to have a high number of inactive users.