The main problem is e-beam litho is extremely slow. It might take ~1 day to do a single photolithography step for a 1x1cm chip, whereas an EUV machine can pattern a 300mm diameter silicon wafer in < 1 minute. (The next problem is making everything reliable. Billions of transistors (a modern CPU) needs a failure rate per transistor of better than 1e-9.)
Maybe that's enough for extremely-low-volume production?
[1] https://mobile.twitter.com/szeloof/status/154993704406717235...