There are plenty of reasons why any figure would hide his identity. Manga is a big deal in Japan and thus many authors try to hide their identity, especially before they are popular. On a side note, I've heard that a lot of Japanese are uncomfortable being a public figure and want to keep their private life private. 
Some of the reasons why Mangakas hide their identity may be as follows:
Content: Manga have a variety of content and much of it may be contentious or even downright controversial. Not wanting to associate their work with "real life" writers utilize pen names to avoid the hassle associated. Its distressingly common problem that people don't get that a Character's POV is NOT the author's (Its just writing). Anonymity in such cases allows mangakas to be a lot more creative.
Another example is genre such as Hentai, which is something you don't want to be known for.
Diversity of Work: Do you want to read a Shoujo Manga from a author known for Shounen works? Googling a name of an author for Children will not associate them with their other works. A pen names also allows an author to be free of the expectations their more popular work may have set.
Bias: This is where I can give a real life example of the top of my head. Horumu Arakawa author of probably the most popular Shounen Manga of all time (Fullmetal Alchemist) used a male pen name because her being a female didn't match the nature of her work and a pen name would help bias against her work at bay.
This is not that uncommon in Japanese Manga industry. A couple of examples.
The writer of Deathnote another popular manga is an unknown! Tsugumi Ohba. Before the author profiles in Bakuman, even his gender was unknown.
Shin Kibayashi is famous for using different pen names. The wiki lists several of them