The checkmarks mean that those composites are indeed in use.
You can display all layers, all renovation status etc in 3D and then use Find & Select to find elements using those composites. I imagine if you find one, you will see where all of the others are in use.
You can look at each individual tool (with nothing selected!) as Laszlo and Barry stated and see if the composites are in use with the current (now default) settings.
Your idea of checking hotlinks is also a good one. Delete all of the hotlinks in a copy of your file and see if the attributes are still in use. If the checks are gone...then open each hotlink individually as a standalone file to sort it out. Hotlinked modules do bring along any attributes inside of them... so you probably have to delete these attributes in each module first anyway. (Attribute management = coordination with hotlinked modules requires careful attention as we are all still wishing for a shared attribute functionality.)
If you created any of your own library parts (or someone else did) by saving walls, slabs etc etc that might have used composites... and that part is placed in the project, the composite will show as in use. Finding it will be very challenging.
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