...Will you still be able to scan the planet?

No.
At least that's how it is supposed to work.

On my last scan run I scanned a C 17xMR Plasma with over 10k cloak while I FOR SURE didn't have over 10k scan... Cloak is broken.

1. the cloak on planets owned by inactive players are nullified
2. the cloak bonus from legion bonus might not apply immediately when a player joins a legion(thou it is displayed as if it is) it might take up to one hour.

If cloak fails for whatever reason and result in a loss of planet, the original owner can msg Dan for a replacement.

How is the original owner supposed to know if the opponent had more scan than the planet's cloak? Let alone prove it?

Suppose the cloak is 40K. How does one attempt to have higher scan?

that, currently 24k+ or so would be around bar(thou wiki isn't updated so..), thou 15k+ I'd ask the person who invaded the planet. It certainly doesn't hurt them any if you get a shiny new planet for free(as the replacement is newly generated and the invader does not lose anything) so they just might answer.