Could number of years in Phd affect your chances to get employed in academia?
If you want to do the doctorate, then just do it. Never mind about the rest. While a few people might question the time, I think most realize that there are a lot of reasons that it can take longer than expected. Everything from funding to supervisor issues, to health reasons. Changing universities or programs. 

It is what it is. There are so many more things that can effect "employability" that it shouldn't be a consideration. The general state of the economy in the years after you graduate has a much bigger effect, I think.