Did Carl Sagan's popularisation of science affect his research career negatively and is there any evidence?
Carl Sagan's writing for the general public was frequently criticised by other scientists, so one could imagine that it may have affected peer review for funding, nominations, etc. (just a possibility).
It is doubtful that Carl Sagan's popularization of science affected his funding or access to resources in any meaningful way, as he was so well established by the time he became a public figure that it would have been quite difficult to discredit him sufficiently to make any real financial difference. He was also known for his skepticism, a reputation that made him a difficult target for anyone trying to discredit his science.
Sagan was an adviser to NASA almost from the program's inception, and his contributions there were various and valued, as evidenced by the number of awards he was given by NASA. His petition to support SETI (Search for Extraterrestrial Intelligence) was signed by seventy fellow scientists including seven Nobel laureates, and was published in the prestigious journal Science; this is evidence of the levels of respect and support he commanded in his field. The advance paid to him for the novel Contact was two million dollars, before he had written a single word - there is no evidence of money issues in either his personal or his professional life.
The only evidence we have of Sagan's popularity affecting his career is the fact that he was not voted into the National Academy of Sciences; his nomination to that organization is known to have generated some serious debate. But it would be good to keep in mind that just before this occurred the eminent physicist Richard Feynman, who had a bit of a reputation for popularization as well, resigned from the National Academy as a protest over their nomination and selection processes, which are known to be highly political in nature. Sagan, like many great intellects, did not play political games well. He was an outspoken advocate of marijuana use and legalization, and his personal life was both stormy and at times not very private. His nomination to the Academy was supported by the astronomers, his actual scientific peers, but members of other branches of science were able to raise enough objections to prevent him from getting the two-thirds vote necessary for membership.