Hiding layers will only hide themduring authoring - you could make those layers be Guide Layers and they would not be output. As for the MoivieClip nested animation ot playing back in the GIF... change its behaviour to that of a Graphic Symbol and then it should render the internal animation on output.
I think I figured it out... When I simply used the Export/Export Animated GIF, I got no motion from neither my movieclip symbol *nor* a Graphic symbol version of the same loop I wanted to use. I tried different formats of exporting/publishing but when I used Export/Export Video/Media and chose and Animated GIF there - my looping symbol worked, even as a movieclip.
So much more to learn...
Besides the guide approach mentioned by Joseph, it's possible to prevent Animate from publishing hidden layers by going to File > Publish Settings... (Ctrl/Cmd + Shift + F12) and unchecking Include hidden layers.