Absolutely. I have a few TV series with hundreds of episodes. Look on this page
http://www.serviio.org/index.php?option ... icle&id=12 for file naming conventions.
Now if you mean a single media file with more than one episode in that file, I haven't been successful with any specific naming. I do have one series that has to episodes in a single file, and have just stuck with naming it with the first of the two. I may just split the file into two separate files.