The 1N400X is so common that its used everywhere, including in applications where component selection is taken very seriously.
In some products, where a 1N4001 was spec'ed for the original design, the paperwork required and rectification needed to change the component to 1N4007 can be quite expensive.
So manufactures will continue to supply the parts even when better options exist. In some cases the manufacture may have signed a contract to product the component for 20 years or more as a condition for their product being chosen over competitors.
The real question is..
Nowadays, is a 1N4001 is any different to a 1N4007, or is it just the text stamped on the outside
Though they probably are different, as Rerouter pointed out, some applications rely on the breakdown voltage.