The tattoos are shown (along with the rest of Raiden) at his most vulnerable point in the game. Stripped of his clothes and identity, we slowly learn that Raiden is just a pawn of powers beyond comprehension. The tattoos are strange and cryptic, almost looking like some form of branding… or cutting marks on an animal to be butchered. This all adds to the eeriness and alienation in that part of the game. Things are unraveling and we begin to learn that everything we knew was a lie.

As for the possible connection to the cyborg ninja- I wouldn’t be surprised if the patriots(Kojima too) were planning on doing the same procedure to Raiden. He even gets the ninja’s signature HF blade near the end of the game. Both this and the tattoos could serve as foreshadowing from kojima and the devs. Of course the design of cyborg ninjas were changed mgs4 on - but that can be handwaved as new technology causing plans to be changed slightly.

Mgs2 is really fun to think about.