1. You can use page names (file names) different from the title of the page with configuration 'useheading'. http://www.dokuwiki.org/config:useheading
The problem: some functions still do not work with useheading, e.g. the "Ajax" popup menu of the search bar uses filenames, not headings.
2. Do you have shell access to the server? Then a shell script moving all files into subdirectories should be easy. If you have links between the pages you also need to correct all the links as well: The script should replace all ''[[a' by ''[[a:a' and so on in the content, e.g. by using perl or awk.
But I am not sure whether this will solve the problem: characters are not distributed evenly, so some directories will have less, some more files; the largest one maybe 10,000. You will have the same problem again if your dictionary grows. A dictionary might be one of the rare cases where one should rather use a wiki with a database.
3. Insert an empty line after '"PUNG".'