If the kitchen is small and the cabinets are brown, I would put them right up to the ceiling and if the bottom is high enough to allow, I would put an open shelf just below them. It is so convenient to have 1 open shelf right at hand!

Tough choice because both are lovely.
What you might want to do is
look at what others have done. (hopefully they will post
pics) and think about the look you want. I love the
furniture feel of no soffits but I have seen some great
kitchens with them. Look over your favorite kitchens
and notice which ones have the soffit and which don't.
And that can help you decide.

Meanwhile I have posted a few pics that might help.
Sorry they are not the med brown shaker cab you are
thinking, but at least you can get some ideas of what
you might do in your own kitchen.

Oh but first look at the before and after pics....
With a Soffit

Now No Soffit

And here is a gorgeous kitchen with a Soffit
Bluestoneconstruction

I love white kitchens had to toss this one in too.
I love the dramatic soffits here. Expensive but so pretty.
{{!gwi}}

Lovely
No Soffit

Accent lighting behind the soffit. Amazing

Shelf Soffit. Interesting idea...
{{!gwi}}

No Soffit

With a soffit

Good luck choosing.
~boxerpups

Here is a link that might be useful: Great pics from GW about molding or not

boxerpups, thank you for the pictures! I love your kitchen and I really like how it looks going up to the ceiling with the molding. I got the revised pricing today and it will end up costing a few hundred dollars more, but I think it will be worth it. The space will be very open and I think it will look more finished.

Hi AnnieZZ,

Oh dear, that is not my kitchen.
It is lovely but not mine. That is a picture from
my collection of kitchens I like or ideas I like.
Sorry about the confusion.

My kitchen is white and I have dental molding up to the
ceiling. I did not have room for a soffit.

You will love the look of the molding that you
are going to pay a little extra for. It will be gorgeous.

~boxerpups

I agree with Emily_Mb. The two most essential words in your OP are "small" and "shaker". So, I would do taller cabinets, either 39" or 42", no soffit, and with a simple molding that fills it up to the ceiling. You say your kitchen is small. I think soffits are nice when you have a large kitchen, but a waste of precious space in a small kitchen. Also, I think you can never have too much storage in a kitchen, and 36" cabs won't give you a whole lot, especially for taller items like wine glasses or cereal boxes. You say your kitchen is Shaker. Huge moldings are not suited to the simple Shaker style, and (just MHO!) I think they are too fussy for a kitchen, and more suited for a library or den.

If anyone says that tall cabinets aren't good because the top shelves are too high, well, I don't agree. First, the top shelves are great for storage of infrequently used items (holiday dishes, light bulbs, etc.). Second, unless you're tall, you'd need a stepstool for the top shelves of 36" cabinets anyway, so needing a stepstool for a 39" or 42" doesn't change anything.