By today's standards, Troughton's hair was horrible. But I would challenge you to look at styles over the decades. I laugh at old pictures of myself. Secondly, there was an underlying effort to put more humor into the series. I think the hair style fit in with that. If you have seen the 5th anniversary special, "The Three Doctors", Hartnell describes his future selfs as, "the dandy and the clown." Just part of the evolution of the show. What about Pertwee's hair?
The second doctor is known as the cosmic hobo. His haircut and apparel fit that description to show he gets by with what he has even though it doesn't match styles with each other.
