You have to bear in mind that there are a range of publishers and a range of magazines. Photographers working for Vogue are in an entirely different situation from ones working for small circulation specialist publications. Many publishers make their money from lots of small magazines and they have to control their costs severely - anything different is extra expense.
Speed and ease of transmission matter for newspapers and other news media, so they use digital. The size of reproduction, the use of b&w or colour and the quality of the paper to be used also matter.
The manipulation issue is not really a technical one, but it's a concern for editors - if their publication is using a photo which has been manipulated they have to know how and why. Airbrushing out a model's zits isn't a problem, but there are obvious risks in photos that make people look bad and even changing the colour of a flower in a gardening magazine could cause problems.
Alan