[Graham Boak]

I can think of five reasons.

1. It was a lot later appearing. Many Ju88s were built before there was any choice in the matter.
2. It also used the more powerful, larger, engines that were in short supply and great demand. The Jumo in the A/D was the 213 not the 211 of the Ju88A/C.
3. What could have been later production was cancelled to allow concentration on fighter production from 1944 onwards.
4. I'm not sure about this, but it is possible that the Ju88 (bomber) was retained in production alongside the Ju188 because it continued to use available engines, and because the loss of production in the changeover was considered more important than the improvement in performance.
5. The Ju188 was ruled unsuitable as a night fighter, because of its glazing. Therefore the Ju88 was retained in production as a fighter. It is fair to say that the later Ju88G was in many ways a Ju188 fighter under another name.

That's four good reasons and one debatable one.