I like 42”+12” uppers with the 12” being glass with lights I think it looks so much better than a space at the top that just gathers dust and stuff and this also will give you max. storage.

39"+12" = room for the crown

Doing 42"+12" will bring you right against the ceiling and you cannot finish the top. If there is a slight variation in the ceiling, it could cause a problem.

How would it look with just 42inch cabinets and moldings that add about 4 inches?

Yes it will look fine. To see examples, go up above and select KITCHEN and then in the Houzz search bar enter 9 ft ceilings. You'll see examples.

We have 48" cabinets with crown. Looks great and cost a bit less than the stacked options.

42" with a "stacked" crown would look great. Maybe 8" or so

Fan Builders. Great renderings to help with dilemma.