That isn't how it works though--look up partial pressures of gases. Helium will continue to escape until its partial pressure is at equilibrium with the external environment, i.e. near to zero, and the external gases will enter until they are at equilibrium with the internal environment. At that point the partial pressure of each gas will be equal on both sides.

What happens to these helium hard drives if you repeatedly cycle the pressure, like by taking the hard drive on an airplane?

Since the partial pressure of helium at ground level and flight level is essentially the same (≈0) there should be very little change, providing the seals are intact. Since they are very securely sealed to contain the helium, changes to the external pressure, unless extreme, should not have any significant effect.

He states that they see one drive that is between 94-99%, but that may be a sensor issue. You'd lose the power savings.

Nit: those are not percentages indicating how much helium left, just some undocumented SMART attribute "raw values", there is no direct way to find out their meaning. (This is what the article text implies too).

The raw attribute values could be for example 100 = good 99 = moderate 98 = degraded, or a log scale similar to decibels etc. Or it could be a bitfield that has no meaning as a decimal number. etc