These are my guesses as to why the cels have not 
been released:

-When the companies who have the rights to the 
cels discussed this and could not agree on 
whether to release the cels or not and/or how to 
distribute the profits, the contracts they signed 
stated that the cels would be put away for X 
number of years (or possibly forever, but that 
seems silly ^^;).

-The companies who own the rights do not have 
time to discuss this issue again since Evangelion 
is an old series (more than 5 years since its 
broadcast on TV in Japan); they would rather 
spend their time and efforts on current projects.

-Even if the cels sell for a lot of money (and we 
have to consider how much the studio gets from 
the sales, not the prices we see from cel 
dealers), the profits would then be divided up 
between the rights holders. Some of those 
companies may consider that it is not worth their 
time to negotiate considering the amount they 
would receive.

-Lastly, grudges between companies (you never 
know, right? ^^;)

---Trebuchet