I am sorry for the inconvenience caused to you.
I would like to inform you that when a image is removed from iPhoto, it is only removed from the iPhoto interface. However, the image does exists in iPhoto Library.
So when you have imported the iPhoto library, all the images has been imported to Lightroom including the deleted ones.
Lightroom doesn't have any plugin as of now for Photos library. So the images which you have uploaded to Photos library after upgrading from iPhoto, Lightroom is not able to recognize them.
And as you have imported the images directly to Lightroom, you are not able to find any metadata or tags.
Hope this helps
You will have to remove the images manually after selecting the images.
Please follow the below link to remove images from catalog.
Hope this helps.