I understand there is a scan limit depending on how many planets are in your data base but how does cloak work?
Does it subtract the scan chance and the cloak or do they apply separately?

For instance if I have a medium chance to find a planet and I have say 1000 scan, does the scan apply a penalty for it being a medium difficulty, then apply the planets cloak? Or does it work as a direct thing like the scan goes through but they have around or over 1000 cloak so the planet stays hidden?

Does planet cloak work stronger then typical ship cloak, or at an equal level?

The generally accepted formula is that if your planet's cloak is greater than the scanner's scan, then they have absolutely no chance of finding your planet.

If your cloak is equal to or less than their scan, the first per-requisite is passed and they have the ability to find your planet, however the chances of actually finding your planet are reduced unless their scan is a good deal greater than your planet's cloaking.

This is what Dan says about how it works