IF the imported graphics are still being used, then when you open a file with a "missing" graphic, FM does ask where the missing file(s) is located and will use this information when searching for other missing graphics in other files of book. You could try creating a temporary superbook that contains many of the files and then doing an update. Otherwise, deleting "unused" Reference pages doesn't really gain you anything (and you could potentially mess up some paratags if they are using any of the reference frames on any of those pages).
When you import formats into FM files from another, FM uses and additive model, i.e. identically named objects are replaced and new ones are added. Nothing is removed.
I find the concept of an "unused" reference page to be murky at best. However, if you know the specific names of the pages that you don't want anymore, it would be a reasonably simple script to delete them as a batch.
You mention that an import doesn't delete any pages... it only adds pages. This is true, but it will also replace any pages of the same name. So, as an interim fix, consider deleting all the offending graphics off of the "unused" pages but do not delete the pages themselves. Then, an import should at least clear up the errors in the destination files. You'll still have the pages hanging around, but maybe who cares?