Considering the real world requirements to achieve a PhD, then yes it's realistic that it will take Howard 2 to 3 years (each season is one year roughly) to gain a doctorates degree.
See https://academia.stackexchange.com/questions/18444/does-a-masters-degree-help-completing-phd-sooner , the second answer for some details on what's required. In short, it takes meeting the Universities requirements, courses, and research. It's not a fly by night certificate. Howard's work would not necessarily count as course credits or anything, but might depending on the University or his Doctorates mentor.
The show has a habit of not explicitly mentioning all the background efforts of the individual cast unless needed (See the question about Penny's pharma rep job), so it's safe to say that Howard is working in his PhD until we are told he stopped or until he completes it.