Huh. I don't see any obvious pitfalls here, the physics and principle of operation are quite simple.

I am struggling to come up with an explanation as to why I haven't heard about this before other than sneaky DOD stuff.

Who would like to bet me a large sum of money that there are currently operation military sats employing this......

EDIT: as epicureanideal pointed out, commenters in the article raised valid points discrediting most of the author's analysis. +/- charged ions get same net kick in the field, comparing proton mass to electron mass is a red herring.

Overall concept still passes sniff test, just needs further analysis. It's going to be all about the angle - you need one ion species to spend more time in the field than the other to get a net thrust

A magnetic scoop with a normal ion thruster might be more practical.

EDIT 2: After further consideration, my concern here is what happens outside the plates. This works for infinite parallel-plate capacitors - you just need to have the field strong enough so one ion species undergoes more net acceleration. In practice the field outside the plates will not be zero and that could spoil everything

EDIT 3: I know nothing. E&M is hard. There will be a current around the outside as you're pumping positive ions to one side and negative to the other. This will induce a magnetic field affecting the ions being pumped through the field. I have no clue what the net effect will be.