Most people are proud of their open source contributions; they're part of your personal brand, and people in the community like to look good/get discovered that way. It builds credibility and shows goodwill.
I use pseudonyms when I wish to speak freely to a larger internet-only community, away from scrutiny by people who know me in real life but may not understand the context of the community in which a discussion takes place. I suppose I would construct an alter ego on Github if I were working on something illegal in my country.
Anything targeted at people who know you should be under the name they know you by. It's not as if pseudonymity defeats Big Data - all they care about is which ads you're likely to click on, whether there is a correct name associated with that profile is of no consequence. And of course anything not done through Tor can still be traced through your ISP's subscriber records. Using a pseudonym on, say, Facebook mostly just inconveniences people. I suppose it could be a reasonable countermeasure against a stalker, but locked-down privacy settings (or just not using Facebook) are probably safer bets.