This is a feature that toonboom studio has and also Pencil2d has. The idea of invinsible strokes is that they are there to allow you to divide a fill into shades. These strokes do not render. And they dont greate a gap between fills.

Possible implementations:
-Add a "slice" mode to the Eraser tool. That lets you slice up a fill into two separate objects. (after bucket tool use).
Currently the erase mode (cut out from objects) creates a gap between the two cell tones and also generates a bazillion nodes making it unmanageable. Doing it with a normal stroke creates a gap too.
-Add a new tool for this that allows users to create invinsible strokes. (before bucket tool use)
Current problems with the bucket tool:
It has the same problem as a bitmap bucket tool (its rgb based fill) - leaving small areas unfilled because of threshold. So the user has to go and manually correct that. Pencil2d's fill tool does not suffer from that problem. More over it allows you to close gaps by using invinzible strokes. The pen tool has autosnapping on the start and end of strokes you make- to reduce the chance of having a gap.
-Suggestion- add "vector based" fill mode. It fills areas precisely on the vector shapes surrounding the area.
Here is a video i made to illustrate the issue better and to show a workaround:
http://www.youtube.com/watch?v=XeFgXKzCOlQ&feature=youtu.be
The bucket tool fill shapes do not change when you move the strokes. In pencil2d if you move a stroke, the fill underneath it changes as well - fills get glued to strokes.
- Suggested design solution- allow bucket tool to create dynamic fills that are glued to the lines above them, if those lines are normal strokes
Now I am aware of all the complicated workarounds to these problems (alt+d and lots of clipping masks, select same color-->combine, etc etc) This stuff is time consuming and a pain in the ass.
For that reason it makes more sense to cartoonists to use something like pencil2d for quick tasks over inkscape. The same cell shading work takes more time to do in inkscape and is more complicated.

My suggestion is to open pencil2d and play with it's vector tools. See what can inkscape borrow. The tools may look unfinished and less advanced than inkscape- but the fact is that they beat inkscape's in terms of efficiency and speed.