Does anyone know if InDesign CS6 displays an alert if you link a missing file to an older version with the same filename? Or, if you link a missing file to a completely different filename? InDesign CS3 would display such an alert, which would give you the chance to catch a potential error. InDesign CS6 seems to link to whatever filename you click on, without question.
Absolutely not. (Re-)Linking a missing file is something you do on purpose, like starting a car. Why should ID complain here?
It will only tell you when linked filed have changed (file name, file size, file dimensions) once you open a document. While working with a document, it will also detect altered links, but only warn in the LINKS panel.
I doubt that the CS3 version will do what you describe. I worked with CS2 and CS4 versions of ID and they all behave the same way here.
This is something you'll have to look after manually.
Probably best to never have files of the same filename.
You could have
or something that makes better sense.
But follow a naming convention.
I have images for the web all the time and I would save it as
this lets me know the right image for the homepage at the correct size.
I suggest you adopt a naming convention for your files to avoid confusions.