People with both styles are in many of my social circles, but they still seem relatively distinct to me.
The two objects of interest are not the same, they're not in the same category, but they're both tied by the same kind of enjoyment for retro things.
So it's not really about which shirts are worn by geeks and hipsters at the same time ...
Depending on where you're at culturally, anime could be relatively obscure.
Hipster is a blanket term that really means something along the lines of "they're doing something unique to others in order to stand out and be 'cool.'" A "geek" may wear a Github or a Mario T-shirt because it's "cool" within their circle, but relatively obscure to the general public.
You could dress up like a 1980s goth kid, which is retro and relatively obscure these days, but I don't think many people would consider that hipster. I think anime t-shirts are similar, even where anime is obscure (also, I think outside of college campuses, anime is universally more obscure than many people believe).
You might be surprised. There used to be a Tumblr blog called LookAtThatFuckingHipster, and it was kind of funny the insane range of people that get submitted there. Part of the silliness of hipster-hating is that it would seem we can't even agree what constitutes a hipster! I remember seeing more than a few emos and goths in the bunch.
I don't know anyone who actually dresses for attention. I know plenty of people who dress unusually though, since I'm part of the rock/goth/alternative community in my city. Every one of them dresses according to their sense of aesthetics. They dress in a way that they think looks good.
I get the feeling that a lot of the people complaining about hipsters are like when you get regular people complaining about modern art or jazz music. Ignorant people making assumptions. I'm not saying I understand hipster fashion, but I at least know that I don't understand it. I find it hard to believe that many people dress in a way that they personally think looks bad in order to be fashionable.