You could try to delete them without moving them to junk or trash (shift+del)

Also Junk-folder (as well as inbox) need to be compacted ones in a while.

I get too many junk mail to delete all one by one.

I often just empty junk and trash and compact in box. I don't think you understand my problem.

I have been using thunderbird for over 16 years and this problem arrived last year. Why now?

I can only guess. Is it IMAP or POP3? What is the size of your Junk-file? Have you compacted JUNK after emptying? If IMAP, How about empty (and compact) it on server as well as trash.

An easy way of knowing the size of a folder is to activate the extra columns in view/layout/folder pane columns and choose what to see, (image)

I copy all junk to junk-folder in Local folders. (You can set it to delete at once in account settings/junk settings). I also just mark deleted as such instead of copying it to trash. That works for me.