Well they built 15,000+ Ju-88s. Pretty sure that wasn't all in 1940. The reasoning on not developing say the Ju 188 was that it would cut back on Ju 88 production.
Ju 88 was arguably an excellent bomber in 1941. A bit less so in 1942. Having trouble though still usable in 1943. In big trouble by 1944.
All those planes probably weren't actually deployed and many were destroyed on the ground or broke down, but if say half of them were shot down in combat that's 30,000 crew.
Maybe make 5,000 Ju 88s and who knows? 3-4,000 Ju 188 or 388 models, and possibly you don't lose as many crew, or waste as many machines. Production capacity doesn't help that much when the dualumin and engines and fuel are all ending up in a smoking heap on the ground a few weeks after the plane is built.
(I've decided that this what-if has merit, and expanded it further: no Ju 88 what so ever)
Perhaps RLM is disappointed once they see the Ju 88 under-performs when all the bells and whistles are on (wing racks + bombs hanging there, blocky & draggy cockpit, defensive positions, dive brakes etc), so they cancel the Ju 88 as-is. Decision is made to expand production and slightly improve the He 111, while sending the request for a new, actually fast bomber with a proper bomb bay, so the big bombs don't mess with aircraft's speed and range that much. Extra resources available untilt the new bomber is around, most importantly the engines the Ju 88 was supposed to get, can be spent on the other projects.
Ju 88 is cancelled some time in mid-1938.