How do EAs deal with having a "weird" appearance?

The "weirdness points" idea describes a real dynamic, for sure. But it isn't everything. For a lot of EAs, an even more precious currency might be "sustainable motivation points". For that reason, EA usually does not recommend donating so much that you live in poverty, or working yourself ragged with no time to relax, but instead preaches a more moderate and achievable path of sustainable donations & effort, which can coexist with a pleasant life. By the same token, EA tries to push people to be more ambitious and seek more influence over the world (through career success and etc), but this isn't a totalizing principle, and I don't think anyone should interpret EA as making an oppressive demand that they subjugate important parts of their personality/presentation/culture/etc in order to become the optimal ladder-climbing achiever. People care about self-expression in many different ways (and, like you say, in different overall amounts), so it's your own call what tradeoffs to make. But IMO, if EA is telling us to be more prestigious/normal/etc, we should interpret that as a friendly marginal nudge, not a totalizing moral obligation.

I think my take would vary depending on the level of weird.

For slightly weird stuff, as discussed in Tessa's answer, it's not actually obvious this is a net cost – the gain in memorability and inferred bravery/independent-mindedness could easily outweigh any costs to credibility.

For very weird stuff, I think it probably is net bad for your expected impact / career prospects, so if you don't care overmuch I'd advise against it. But if conforming to conventional appearance norms is very difficult/alienating/demoralising to you, then you should probably do the weird thing. In that respect, I put it in the same category as having kids, or living in a non-standard location with worse network effects. To quote Julia Wise:

Some things I can do cheerfully. It turns out that giving up children was not one of them. Other people would have no problem giving up parenthood, but I suspect that everyone has something that would cause an inordinate amount of pain to sacrifice.

So test your boundaries, and see what changes you can make that will help others without costing you too dearly. But when you find something is making you bitter, stop. Effective altruism is not about driving yourself to a breakdown. We don't need people making sacrifices that leave them drained and miserable. We need people who can walk cheerfully over the world, or at least do their damnedest.

Now, all that said, what counts as "slightly weird" vs "very weird" will vary depending on the place you live and the sector you work in, and so needs to be evaluated on a case-by-case basis. Academia values conformity in appearance far less than, say, the US Government. And of course different kinds of "weird" will imply different things – kooky vs messy vs uneducated, et cetera.

It's also sadly probably true that if your appearance is unavoidably different from most of the people around you, that will impact how additional voluntary weirdness is perceived – though I'm very unsure how that last thing cashes out in practice, in terms of the impact of marginal weirdness on your reputation.

I think you're right that some people will make prejudiced snap judgments of you if you have cornrows, but my instinct is to say, "screw 'em, they should get over that". I guess I'd check in on how common you expect prejudice to be and how relevant such judgments will be to your career or other goals. For example, are there successful people in your academic field who look the way you want to?

I am a person with weird hair (usually dyed blue-green) and I think there are some social circumstances where this benefits me by making me more memorable, e.g. I was "the girl with green hair who likes math" at one student conference. It also has costs; I think looking like a person who cares about my appearance/self-expression makes me seem less serious to many people.

As one example of navigating this trade-off, I dyed my hair back to a natural colour when I went to the UN Bioweapons Convention in 2017, because it seemed like a context where it was more important to be taken seriously and which might have more formal dress norms. I probably would not do that if I attend again in 2022, since I'll be 5 years older and have more experience in biosecurity.

I try to keep my weirdness to a level that's greater than 0 (in order to push back against stupid norms) but still low enough that I don't incur significant costs.

FWIW, I don't think there's a cost in academia for looking a little bit different if doing so makes you look a bit better (at least if we're talking about within the US – other countries may be different). Yes, an unkept, big bushy beard would presumably be a negative (though less so in academia than in other professions), but stylish hairstyles like Afro buns or cornrows might even be a slight positive. 

To me, reducing your weirdness is equivalent to defection in a prisoner's dilemma, where the least weird person gets the most reward but the total reward shrinks as the total weirdness shrinks.

Of course you can't just go all-out on weirdness, because the cost you'd incur would be too great. My recommendation is to be slightly more weird than average. Or: be as weird as you perceive you can afford, but not weirder. If everyone did that, we would gradually expand the range of acceptable things outward.