Manipulating their perception of you by taking advantage of social cues.

I'm fine with people wanting to dress nicely as long as they realize it's total bullshit that people are judged by their clothes, but want to take advantage of it anyway. It's just human hacking.

I do feel a bit bad when dressing nicely, because I worry that I am contributing to the continuation of the practice of judging people by their clothing.

I don't understand this line of reasoning. When you go on a date, do you pick up the check for your SO? When you go to a bar do you buy a drink for your friends occasionally? Surely you'd rather save that money, but you have to "hack" society's rules so that they will like you.

Maybe you "hack" HR policies that reinforce the use of proper grammar by refining your resume. Or hold the door open for somebody who is behind you when you'd rather just be on your way. Society is full of norms and social cues, and I don't think it's deception to control your behavior to align yourself with them. To not do so out of some notion that we should combat human instinct is rather naive.

I think Benjamin Franklin put it best: "Eat to please thyself, but dress to please others."

It's human hacking when you recognize that the cues you're leveraging are inane and meaningless. Many people believe that the cues themselves are somehow meaningful or significant, and get caught up in the act.

How, exactly, is it naive to try to overcome illogical biases and ways of being manipulated?

Well I guess the fundamental disagreement is that I don't think these biases are best classified as illogical. Yes, if you are being completely objective, two job applicants should be judged solely on the basis of their qualifications. Yet, the one who is more polished is going to get the job ten times out of ten. Perception is simply a fundamental part of decision making, and I think the naivety lies in thinking that any of us are above catering to that perception or that we can somehow convince people to not rely on their perceptions.

It's not total bullshit. It's grounded in evolutionary psychology. We like people who are attractive because that shows that they have good genes and are therefor worth either a) mating with, or b) keeping around for other reasons. Nice clothes help make a good impression if you're in relatively good shape and your body is well proportioned. If you're 100lbs overweight, that tailored tux just makes you look like a penguin.

So you're telling me it's not total bullshit to hire someone for a coding job based on how attractive they are/seem?

Just because we have evolved heuristics for something doesn't mean those heuristics aren't stupid and irrelevant in some contexts.