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Some way to indicate completely empty frames in a layer. Maybe with a thin diagonal line on the head. I thought of making them slightly darker, but that would only work on a light BG. Or making the empty frames only 2/3 as high as the ones with some content. Suggestions?

A tiny red dot in the bottom right corner. Tiny red dots can be spotted from a mile above.

EDIT: Just noticed what layers can look like when compacted. How about the top handle of empty frames (what looks like a sprocket hole) would be red (or a less intrusive color) so they would be visible no matter how compressed the timeline would become.

+1.
An accent color (like a muted red) on the draggable boxes sounds like a good idea to me too.

If we can zoom in the layer (as asked in that topic : http://forum.tvpaint.com/viewtopic.php?f=21&t=6770" onclick="window.open(this.href);return false;), would it be really useful ? I mean : if you could see what's inside an instance, you won't really need any mark on empty heads.

Good point, which shows how related these two items are (ehm). The advantage of having both would be that an empty frames region would still show up as soon as TVP opens with all the layers contracted. This would help someone like me go right to the place where I want to be to continue inbetweening.

In that case, maybe assign by default an image mark to empty instances ?

Something like :
Image mark panel > options > mark all empty instances with "that" color.

Exactly! And a preference to show or not to show zoomed close ups in layer frames. This is getting fancy.