The known.met file is not a relational database. So it processes secuentially all the entries, 30 THOUSAND of them.
When aMule iterates your shared folder, for every file it finds it compares it to the known file list. Which has 30 thousand entries.
I'm sure you can see the problem there.
About your comments on Kad indexing your files: Yes, Kad will index all your files. It will however take a long long, LONG time to do so, so I hope you leave aMule open for several days if you plan the network to index all those files.