One approach to handling the "n/a" situation is to simply tick the item for that day. In your "Prepare for a meeting" example, you'd check it as true even if it's n/a. All tools will handle that situation, and yes you're getting 'credit' but it's often not the end of the world.
There are a small number of 'fuzzy logic' habit trackers that really intrigue me but the usability isn't quite there. The Habit Factor - just too bug ridden and gets in my way. Sciral Consistency - very cool concept but not updated since 2012 (doesn't sync between iOS and web, no web interface, no reporting). HomeRoutine (iOS) very useful for its intended purpose and can be revectored to serve as a habit builder app, but lacking in reporting.
Another interesting app - LeanPD (Lean Personal Development). Doesn't at all get in the way, with an interesting visual reporting style.
I've also played around with Google Forms, which are easy to use and have the benefit of shoving the output into a google sheet for further summarizing etc. to your heart's content.
But the search goes on.