• Such shot sets all data stored in RAMs to all logical "1"

This would have the same practical effect as the power going out. Restart your computer and everything is fine. The big effect here would be on airplanes and so forth -- I imagine it's difficult to do a hard reset of all the electronics while the aircraft is in-flight. However, this answer suggests it is possible.

• Also, hard drives are given instruction to write to all sectors logical "1"

This would have a much larger effect, since most data is stored on hard drives. Individuals would tend to lose everything (not many people keep backups), but corporations would just lose hours to days of data, and could quickly recover most everything.

Because very little personal data is truly important, most people would be largely unaffected after a few days to weeks, since they could just recover the data from corporations who backed it up.

• While the scope of attack is bit "magic", it obeys the laws of physics:

No, it really doesn't.

• The attack is electromagnetic pulse based
• So if a computer is hidden behind something which should prevent electromagnetic pulse, such computer remains fully functional

An EMP is indiscriminate. It will wipe out any and all electronics or none of them. The only question is how sensitive the given electronics are. So if the computer is partially shielded, the most sensitive components will tend to die while the least sensitive will tend to not die. The HDD platters are far from the most sensitive, and anything affecting HDD platters will also affect tape drives and other magnetic media.

What you're thinking of is sending specific signals to a specific part of a hard drive's controller to make it think the OS told it to erase things. But you really can't do that. The radio photons are feet to miles across, so there's no way to make sure a photon hits a specific HDD controller, let alone a specific wire on that controller. Even microwaves are several inches across. By the time you get to EM waves small enough to hit a target wire, we're talking optical light and beyond, which is easily blocked by walls, CPU cases, etc., and isn't readily absorbed into said wires.

Now, sufficiently advanced aliens could hypothetically create an incredibly advanced interference pattern that cleverly hits specific points, even with large wavelength photons. However, this would require billions, if not billions of billions, of photons per bit sent. Because photons have fixed energy amounts, that means such an interference pattern would end up vaporizing everything around the computer, if not the entire planet (conservation of energy says even if there's destructive interference, the energy has to go somewhere).

• Also, the pulse obeys square inverse law, so the more mass is between orbit and the computer, the less effective the attack is.
• The attack is synchronised, covering all the Earth in one shot

The inverse-square laws are about distance, not mass between you and the attacker. This means an attack from 100 km above the planet will have almost zero effect on objects on the other side of the planet (not including the massive planet in the way).

Because everything is synchronized anyways, there are probably dozens to thousands of ships in orbit around the planet. The fewer ships, the further they have to be to get good spread. The more ships, the less distance there is between them. Either way, coverage will be relatively uniform, so the inverse-square law won't be a huge consideration. And the aliens are probably smart enough to concentrate the "bright" spots on the major cities.

• My working meta is 10 metres of (any) mass between computer and orbit to render attack fully uneffective.

Mass between you and the attacker will exponentially decay signal strength, and the coefficient will greatly depend on the material in question, as well as the wavelength of the EM radiation used. The basic form is $I=I_0e^{-\beta D}$ where $I_0$ is intensity at the surface of the material, $D$ is depth into the surface, and $\beta$ is the coefficient for the wavelength and material in question.

Air will have a very low $\beta$ value for most wavelengths, while concrete will have a high $\beta$ value for most wavelengths. Long wavelengths (low frequencies) will tend to have lower $\beta$ values than short wavelengths.

• Also, I am aware of one huge flaw: Computer has to be turned on in moment of attack. The attack has no effect on turned off computers. However, as long as the computer is at least in "sleep" mode, the attack has effect.

This is only a problem if the attack somehow activates the "overwrite" circuits on the HDD controller. If it, realistically, just overloads the physical data structures, it will work on anything whether it's on or off.

• And they know that if we are unable to communicate, the Earth is not going to be accepted and next visit is going to happen in 50 years.

We can build radios out of random crap in your garage in like 10 minutes. This attack won't prevent communication with aliens in orbit.