I've looked and haven't found anything on 'why' Morricone used a couple of aliases over time. My guess (only a guess) is that in 1966 he had 5 or 6 movies come out and (for the same reason Stephen King wrote under the name Richard Bachman) didn't want to appear to be flooding the market.
It's also possible that since Navajo Joe and The Good the Bad and the Ugly both came out in 1966, and Morricone was a former classmate of Sergio Leone's, he didn't want people to think that the two movies were made by Leone.