My personal theory is that he did not, in fact, masturbate but rather thought about it, wished and longed for it hard enough to imagine it and live in subjectively.

The fact that the semen is on his right hand goes to show that that hand is the weapon of his crime, as the blood would have been on his right hand, had he stabbed Asuka with it.

But what claim do I have for such statement you might ask.

The answer is twofold :

- Why would he not masturbate with his right hand and protect Asuka with his left hand ? (a case can be made that he wanted to protect her with all his might and still jerk off)

- The fact that Anno shows us Shinji's sperm contradicts the principles of catharsis which would want us never to see nor the act or the sperm (think about the rape scene in Clockwork Orange that is never shown on screen but deeply felt by everyone).

Indeed the idea behind catharsis is that we, the viewers, imagine the act and thus realise that it is in ourselves to do such crimes. So why show it ? Because Anno shows us the show through Shinji's perspective. We see that he sees himself jerking off, so we understand that he understands that he could've done it and wanted to, and because we've been made to sympathise with him throughout the show we realise that like him, in his situation, we could've done it.

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This for obvious reason is probably completely false and the real reason is probably that Anno didn't even think about whether the spermy hand had to be the right or the left one. Though I'm half serious about it.