This is just a slight annoyance, but I am wondering if this affects scanning in any way. I have 351 planets to look through, but my ship says I have scanned 366 planets. I know for a fact that I have purged well over 15 planets since my last scan spree.

What is causing this mix up in numbers and does it affect my scanning?

the number of planets specified in the ship stats window only updates when you click the scan button... purging planets doesn't update it...

go click scan once... regardless of whether you succeed or fail, it will update to the current correct number

So it waits until I am able to scan again?
( I remove all scan modules when I'm done scanning, because I don't currently have the room on my ship for them to be on 24/7)

pretty much...