I'm just testing adding LDAP to our current use of Shibboleth on one of my systems. They seem to work alongside each other happily enough - the tricky part is providing a log in page that won't confuse people.
I've hacked the index page to emphasise the most used auth, but that's definitely not best practice - there might be renderers/templates to override as a better approach.
My long-term plan is to make a plugin that provides a single login form that sends logins to the right plugin based on RegEx patterns (e.g. Shibboleth uses abcdef12, manual uses 123456, etc.), but I've not made time for it yet.