As far as I know, Nadesico production cels fall 
under the category of Neon Genesis Evangelion 
cels... they were never meant to leave the studio 
and thus any cels you see on the market are 
highly priced because they are rare... and any 
cels you see somehow leaked out of the studio 
through unofficial means.

As with Evangelion, there are official machine-
reproduced cels and rare limited edition hand-
painted reproduction cels for Nadesico.  Because 
of the presence of these type of reproduction 
cels, that's why I tend to believe that actual 
Nadesico production cels were never intended to 
be released to the market (as with Evangelion).

Obviously, though, Evangelion cels are more 
highly sought (and probably Gainax kept a tighter 
lid on those cels, which made them rarer), which 
is why the prices for Evangelion production cels 
can be considerably higher than Nadesico cels.

As for your question about the Nadesico Movie, I 
tend to believe that a good portion was produced 
with cel animation, although I believe that Xebec 
has kept a strict security on cels from this 
movie.  There was an exhibition of Nadesico Movie 
cels at Anime Expo in 2000 (when Keiji Goto was a 
guest), although they may have easily been hand-
painted reproductions (I didn't take a good look).

You should also keep in mind that studios are 
capable of maintaining very tight security over 
cels from certain anime titles.  For instance, 
cels from the recent Vampire Hunter D (Bloodlust) 
movie have not appeared on the market anywhere, 
with the exception of Anime Link (for which they 
appeared to have landed a special agreement with 
the rights-owner).  Since the film was actually 
completed a few years ago already but no cels 
have appeared on the market until this year, I 
would have to say that the security over the cels 
has been very good.