Hi Robert, i think it does seal it pretty well, the oil based markers seem to work even better. It will wear though and I wash my hooks and give a spray of inox after each trip. You can touch up the pen work then also. That said i'll often be lazy after a big trip and forget to do it and man, they do rust up pretty quick.
Yeah absoultely the hooks can be touched up - when i was using SJ51's i used to dremel the "wings" of the apparent cutting tip off to give a finer guage hook. I also can't help but touch up the point of even new hooks if i'm debarbing them - need to be careful though as while there is some sharpness to be gained it only takes a small slip take the tip right off and it can be a lot of work to get it back even close to what it was like coming out of the packet. I also carry a small stone to touch up the tips of hooks on a trip just in case they dull or get knocked.
Not sure on the other solution you have in mind, I think the bill fishers use a type of tape that has like a sacraficial anode type effect so that their hooks don't dull while being trolled around all day - too cumbersome a solution for GT lures though.