Unless you are using shape layer modifiers and animators like repeaters or are extruding the layers there is no advantage to converting vector layers to shape layers. There are a host of disadvantages to design and color.
That said, what you get is what you get. There are no groups that come through. The layers will be created in the right order but lot's of things may get lost in the process. If you need groups you'll have to build them inside the shape layer with the Group add on.
When I import a file into AE from Illustrator and select "Create shapes from vector layers". Is it possible to maintain the actual groups from Illustrator?
not really. the names won't be retained and also the structure will be that each object will be in it's own group containing it's path, fill and stroke - the Ae's shapes group default bundle.
I know I can organise my ai grups in layers and select "Convert to layered comp", but I want shape layers.
how about this: for each group you want, create a layer and place it inside it. it will be much more manageable later on when you do convert to shapes. or use this handy script: Explode Shape Layers 3 - aescripts + aeplugins - aescripts.com that will do this for you in Ae after the fact and offer more tools to manage your shapes.
Is there any other way than selecting "Create shapes from vector layers" and then manually regroup everything?
nope. but keeping your Ai file organized is the way to go. https://helpx.adobe.com/after-effects/using/preparing-importing-still-images.html#preparin g_and_importing_illustrator_files
Didn't this use to work the other way around, so ae only saw the top ai groups?
highly unlikely. you are probably confusing this with the fact that Ai can only see the top most layers and not sub layers.
Thank you both for answers.