So I paid 1000$ to get eye surgery for the eagle eye perk.
Doc said something about irritated eyes and whatnot, but I do not see a negative indicator about this.

My looting chances are super low everywhere and my sneak chances are high (although im not hiding).
It has been 2 days since surgery, I still get low looting chances.

https://imgur.com/a/wmp1OxI

Are you looting near the city, or further afield? Looting near the city always has low chances because everything in the area has been picked clean already. If it's not that, then a bug I guess, since Eagle Eye is supposed to increase your chances, not decrease it.

It could be that there is a debuff associated with "irritated eyes", and it just doesn't show up because you don't have the medical perk (or whatever it's called). If that's the case then hopefully it'll come good in a few days or so.