Yes, AE automatically de-interlaces your footage because (from the AE manual)
Separating fields is critical if you plan to make significant changes to the image. When you scale, rotate, or apply effects to interlaced video, unwanted artifacts, such as crossed fields, are often introduced. By separating fields, After Effects accurately converts the two interlaced frames in the video to noninterlaced frames, while preserving the maximum amount of image quality. Using noninterlaced frames allows After Effects to apply edits and effects consistently and at the highest quality.
You can re-interlace the footage, if necessary, when you render your composition.
The deinterlacing can be turned off in the Interpret Footage dialog, but you shouldn’t do that.
Joey Foreman
Editor/Compositor/VFX Artist