Thanks again for your help.
I have solved my problem and I think it was caused by third party software.
I had two bundles enabled in my Mail in Library/Mail/Bundles; they were MailTags and Herald, both supposedly El Capitan compatible.
I removed both, kept all folders checked in Spotlight preferences in System Preferences, tried a Spotlight search and hey presto Spotlight began to index properly and everything is back to normal in Mail.
I've re-installed Herald and everything still works properly. I haven't re-installed MailTags.
Having removed both at the same time I can't be 100% sure it was MailTags that was causing the problem, but I strongly suspect it was.