I don’t use version 3. Therefore, the following advice is for version 2.
To disable the filter, you remove the check mark in the 'enabled' column.
To delete the filter, select it and then click on 'delete' on the right-hand side.
There is no built in way to sort the filters, at least, not that I've noticed. Proper naming would make it easier for you to find the filters you want to disable, as well as properly creating and combining filters that perform similar functions so that you don't have/need so many that you can't find them.
Do you use your Junk Filter? This may also help to cut down on such a large number of filters.
As for better advice, the mozilla support forums would be much more helpful at http://www.mozillamessaging.com/en-US/support/
since this is a text to speech support forum, and it has nothing to do with Thunderbird.