1.Ae imports only main layers when it comes to illustrator. Whatever is inside will remain merged inside the layers. If you want to have access to the layer's content as separate graphics, you will have to place it in a different layer in illustrator or use "Create shapes from vector layer" which will convert it to shapes but still inside one shape layer's content heirarchy.
2. Ai layers are imported as pixels unless you toggle the continuously rasterize switch in the switches panel
you should read here about preparing your illustrator artwork: Preparing and importing still images in After Effects
Is there any difference in functionality between layers made these two ways (changed in illustrator vs shape layers in AE)?
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Here are a few differences in functionalit:
• An illustrator layer does not have accessable vector data meaning path and vertices you can manipulate . A shape layer does.
• Shape layers have content structure similar to Ai layers with ability to stack fill and stroke and changing them right in Ae.
• Shape layer have shape operators that can be very useful for creating certain appearance or animation.
• Shape layers have additional features that are available if you create them as parametric and not bezier. they could be very useful that animators would even prefer to create vectors from scratch in Ae vs starting in illustrator. Check out the adobe series with motion graphics designer Evan Abrams: https://m.youtube.com/playlist?list=PL79TBmLa4lTQ-C8ubzeiUZAeyhdgYEmNr and also animator James Curran: https://m.youtube.com/results?q=James%20Curran%20&sm=3
this is a heavy topic so to get more information I suggest you type "shape layers" in the search field at upper right corner of the Ae interface and read the help files.