You sure can. Check out the attached image, I know it's not cel-shaded, but more of a hand-drawn look. It's from my winning September FPSC Level Competition entry. If that is possible, then cel-shaded will be possible also. Here's a link to the level: http://www.ozarkgames.com/fpscfolder/september06/benjamin/september.exe. Check it out, but do not use any of it for your own games.
That's the good news
Now the bad news
It cannot be done through a script or by modifying the source code, it's a matter of (re)texturing every entity & segment you use in the game. So you have to create cel-shaded textures (just like I have created hand-drawn textures) and apply those to every entity and segment in your game. That takes a lot of work, but if done correctly, it creates something beautiful.
That also pretty much answers your last question, yes the engine can handle it.
I'm pretty sure this is not what you were thinking of, but it's the only way, perhaps in future that may change and we will have different rendering options in FPSC.
